2 // FORESTER -- software libraries and applications
3 // for evolutionary biology research and applications.
5 // Copyright (C) 2008-2009 Christian M. Zmasek
6 // Copyright (C) 2008-2009 Burnham Institute for Medical Research
9 // This library is free software; you can redistribute it and/or
10 // modify it under the terms of the GNU Lesser General Public
11 // License as published by the Free Software Foundation; either
12 // version 2.1 of the License, or (at your option) any later version.
14 // This library is distributed in the hope that it will be useful,
15 // but WITHOUT ANY WARRANTY; without even the implied warranty of
16 // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
17 // Lesser General Public License for more details.
19 // You should have received a copy of the GNU Lesser General Public
20 // License along with this library; if not, write to the Free Software
21 // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
23 // Contact: phylosoft @ gmail . com
24 // WWW: www.phylosoft.org/forester
26 package org.forester.test;
28 import java.io.ByteArrayInputStream;
30 import java.io.FileInputStream;
31 import java.io.IOException;
32 import java.util.ArrayList;
33 import java.util.Date;
34 import java.util.HashSet;
35 import java.util.Iterator;
36 import java.util.List;
37 import java.util.Locale;
40 import org.forester.application.support_transfer;
41 import org.forester.development.DevelopmentTools;
42 import org.forester.evoinference.TestPhylogenyReconstruction;
43 import org.forester.evoinference.matrix.character.CharacterStateMatrix;
44 import org.forester.evoinference.matrix.character.CharacterStateMatrix.BinaryStates;
45 import org.forester.go.TestGo;
46 import org.forester.io.parsers.FastaParser;
47 import org.forester.io.parsers.GeneralMsaParser;
48 import org.forester.io.parsers.HmmscanPerDomainTableParser;
49 import org.forester.io.parsers.HmmscanPerDomainTableParser.INDIVIDUAL_SCORE_CUTOFF;
50 import org.forester.io.parsers.nexus.NexusBinaryStatesMatrixParser;
51 import org.forester.io.parsers.nexus.NexusCharactersParser;
52 import org.forester.io.parsers.nexus.NexusPhylogeniesParser;
53 import org.forester.io.parsers.nhx.NHXParser;
54 import org.forester.io.parsers.phyloxml.PhyloXmlParser;
55 import org.forester.io.parsers.tol.TolParser;
56 import org.forester.io.writers.PhylogenyWriter;
57 import org.forester.msa.Mafft;
58 import org.forester.msa.Msa;
59 import org.forester.msa.MsaInferrer;
60 import org.forester.pccx.TestPccx;
61 import org.forester.phylogeny.Phylogeny;
62 import org.forester.phylogeny.PhylogenyBranch;
63 import org.forester.phylogeny.PhylogenyMethods;
64 import org.forester.phylogeny.PhylogenyNode;
65 import org.forester.phylogeny.PhylogenyNodeI.NH_CONVERSION_SUPPORT_VALUE_STYLE;
66 import org.forester.phylogeny.data.BinaryCharacters;
67 import org.forester.phylogeny.data.BranchWidth;
68 import org.forester.phylogeny.data.Confidence;
69 import org.forester.phylogeny.data.Distribution;
70 import org.forester.phylogeny.data.DomainArchitecture;
71 import org.forester.phylogeny.data.Event;
72 import org.forester.phylogeny.data.Identifier;
73 import org.forester.phylogeny.data.PhylogenyData;
74 import org.forester.phylogeny.data.PhylogenyDataUtil;
75 import org.forester.phylogeny.data.Polygon;
76 import org.forester.phylogeny.data.PropertiesMap;
77 import org.forester.phylogeny.data.Property;
78 import org.forester.phylogeny.data.Property.AppliesTo;
79 import org.forester.phylogeny.data.ProteinDomain;
80 import org.forester.phylogeny.data.Taxonomy;
81 import org.forester.phylogeny.factories.ParserBasedPhylogenyFactory;
82 import org.forester.phylogeny.factories.PhylogenyFactory;
83 import org.forester.phylogeny.iterators.PhylogenyNodeIterator;
84 import org.forester.protein.Protein;
85 import org.forester.sdi.SDI;
86 import org.forester.sdi.SDIR;
87 import org.forester.sdi.SDIse;
88 import org.forester.sdi.TaxonomyAssigner;
89 import org.forester.sdi.TestGSDI;
90 import org.forester.sequence.BasicSequence;
91 import org.forester.sequence.Sequence;
92 import org.forester.surfacing.TestSurfacing;
93 import org.forester.tools.ConfidenceAssessor;
94 import org.forester.tools.SupportCount;
95 import org.forester.tools.TreeSplitMatrix;
96 import org.forester.util.AsciiHistogram;
97 import org.forester.util.BasicDescriptiveStatistics;
98 import org.forester.util.BasicTable;
99 import org.forester.util.BasicTableParser;
100 import org.forester.util.DescriptiveStatistics;
101 import org.forester.util.ForesterConstants;
102 import org.forester.util.ForesterUtil;
103 import org.forester.util.GeneralTable;
104 import org.forester.ws.uniprot.DatabaseTools;
105 import org.forester.ws.uniprot.SequenceDatabaseEntry;
106 import org.forester.ws.uniprot.UniProtTaxonomy;
107 import org.forester.ws.uniprot.UniProtWsTools;
108 import org.forester.ws.wabi.TxSearch;
109 import org.forester.ws.wabi.TxSearch.RANKS;
110 import org.forester.ws.wabi.TxSearch.TAX_NAME_CLASS;
111 import org.forester.ws.wabi.TxSearch.TAX_RANK;
113 @SuppressWarnings( "unused")
114 public final class Test {
116 private final static double ZERO_DIFF = 1.0E-9;
117 private final static String PATH_TO_TEST_DATA = System.getProperty( "user.dir" )
118 + ForesterUtil.getFileSeparator() + "test_data"
119 + ForesterUtil.getFileSeparator();
120 private final static String PATH_TO_RESOURCES = System.getProperty( "user.dir" )
121 + ForesterUtil.getFileSeparator() + "resources"
122 + ForesterUtil.getFileSeparator();
123 private final static boolean USE_LOCAL_PHYLOXML_SCHEMA = true;
124 private static final String PHYLOXML_REMOTE_XSD = ForesterConstants.PHYLO_XML_LOCATION + "/"
125 + ForesterConstants.PHYLO_XML_VERSION + "/"
126 + ForesterConstants.PHYLO_XML_XSD;
127 private static final String PHYLOXML_LOCAL_XSD = PATH_TO_RESOURCES + "phyloxml_schema/"
128 + ForesterConstants.PHYLO_XML_VERSION + "/"
129 + ForesterConstants.PHYLO_XML_XSD;
131 private final static Phylogeny createPhylogeny( final String nhx ) throws IOException {
132 final Phylogeny p = ParserBasedPhylogenyFactory.getInstance().create( nhx, new NHXParser() )[ 0 ];
136 private final static Event getEvent( final Phylogeny p, final String n1, final String n2 ) {
137 final PhylogenyMethods pm = PhylogenyMethods.getInstance();
138 return pm.obtainLCA( p.getNode( n1 ), p.getNode( n2 ) ).getNodeData().getEvent();
141 public static boolean isEqual( final double a, final double b ) {
142 return ( ( Math.abs( a - b ) ) < Test.ZERO_DIFF );
145 public static void main( final String[] args ) {
146 System.out.println( "[Java version: " + ForesterUtil.JAVA_VERSION + " " + ForesterUtil.JAVA_VENDOR + "]" );
147 System.out.println( "[OS: " + ForesterUtil.OS_NAME + " " + ForesterUtil.OS_ARCH + " " + ForesterUtil.OS_VERSION
149 Locale.setDefault( Locale.US );
150 System.out.println( "[Locale: " + Locale.getDefault() + "]" );
153 System.out.print( "[Test if directory with files for testing exists/is readable: " );
154 if ( Test.testDir( PATH_TO_TEST_DATA ) ) {
155 System.out.println( "OK.]" );
158 System.out.println( "could not find/read from directory \"" + PATH_TO_TEST_DATA + "\".]" );
159 System.out.println( "Testing aborted." );
162 System.out.print( "[Test if resources directory exists/is readable: " );
163 if ( testDir( PATH_TO_RESOURCES ) ) {
164 System.out.println( "OK.]" );
167 System.out.println( "could not find/read from directory \"" + Test.PATH_TO_RESOURCES + "\".]" );
168 System.out.println( "Testing aborted." );
171 final long start_time = new Date().getTime();
172 System.out.print( "Hmmscan output parser: " );
173 if ( testHmmscanOutputParser() ) {
174 System.out.println( "OK." );
178 System.out.println( "failed." );
181 System.out.print( "Basic node methods: " );
182 if ( Test.testBasicNodeMethods() ) {
183 System.out.println( "OK." );
187 System.out.println( "failed." );
190 System.out.print( "Basic node construction and parsing of NHX (node level): " );
191 if ( Test.testNHXNodeParsing() ) {
192 System.out.println( "OK." );
196 System.out.println( "failed." );
199 System.out.print( "NH parsing: " );
200 if ( Test.testNHParsing() ) {
201 System.out.println( "OK." );
205 System.out.println( "failed." );
208 System.out.print( "Conversion to NHX (node level): " );
209 if ( Test.testNHXconversion() ) {
210 System.out.println( "OK." );
214 System.out.println( "failed." );
217 System.out.print( "NHX parsing: " );
218 if ( Test.testNHXParsing() ) {
219 System.out.println( "OK." );
223 System.out.println( "failed." );
226 System.out.print( "NHX parsing with quotes: " );
227 if ( Test.testNHXParsingQuotes() ) {
228 System.out.println( "OK." );
232 System.out.println( "failed." );
235 System.out.print( "NHX parsing (MrBayes): " );
236 if ( Test.testNHXParsingMB() ) {
237 System.out.println( "OK." );
241 System.out.println( "failed." );
244 System.out.print( "Nexus characters parsing: " );
245 if ( Test.testNexusCharactersParsing() ) {
246 System.out.println( "OK." );
250 System.out.println( "failed." );
253 System.out.print( "Nexus tree parsing: " );
254 if ( Test.testNexusTreeParsing() ) {
255 System.out.println( "OK." );
259 System.out.println( "failed." );
262 System.out.print( "Nexus tree parsing (translating): " );
263 if ( Test.testNexusTreeParsingTranslating() ) {
264 System.out.println( "OK." );
268 System.out.println( "failed." );
271 System.out.print( "Nexus matrix parsing: " );
272 if ( Test.testNexusMatrixParsing() ) {
273 System.out.println( "OK." );
277 System.out.println( "failed." );
280 System.out.print( "Basic phyloXML parsing: " );
281 if ( Test.testBasicPhyloXMLparsing() ) {
282 System.out.println( "OK." );
286 System.out.println( "failed." );
289 System.out.print( "Basic phyloXML parsing (validating against schema): " );
290 if ( testBasicPhyloXMLparsingValidating() ) {
291 System.out.println( "OK." );
295 System.out.println( "failed." );
298 System.out.print( "Roundtrip phyloXML parsing (validating against schema): " );
299 if ( Test.testBasicPhyloXMLparsingRoundtrip() ) {
300 System.out.println( "OK." );
304 System.out.println( "failed." );
307 System.out.print( "phyloXML Distribution Element: " );
308 if ( Test.testPhyloXMLparsingOfDistributionElement() ) {
309 System.out.println( "OK." );
313 System.out.println( "failed." );
316 System.out.print( "Tol XML parsing: " );
317 if ( Test.testBasicTolXMLparsing() ) {
318 System.out.println( "OK." );
322 System.out.println( "failed." );
325 System.out.print( "Copying of node data: " );
326 if ( Test.testCopyOfNodeData() ) {
327 System.out.println( "OK." );
331 System.out.println( "failed." );
334 System.out.print( "Basic tree methods: " );
335 if ( Test.testBasicTreeMethods() ) {
336 System.out.println( "OK." );
340 System.out.println( "failed." );
343 System.out.print( "Postorder Iterator: " );
344 if ( Test.testPostOrderIterator() ) {
345 System.out.println( "OK." );
349 System.out.println( "failed." );
352 System.out.print( "Preorder Iterator: " );
353 if ( Test.testPreOrderIterator() ) {
354 System.out.println( "OK." );
358 System.out.println( "failed." );
361 System.out.print( "Levelorder Iterator: " );
362 if ( Test.testLevelOrderIterator() ) {
363 System.out.println( "OK." );
367 System.out.println( "failed." );
370 System.out.print( "Re-id methods: " );
371 if ( Test.testReIdMethods() ) {
372 System.out.println( "OK." );
376 System.out.println( "failed." );
379 System.out.print( "Methods on last external nodes: " );
380 if ( Test.testLastExternalNodeMethods() ) {
381 System.out.println( "OK." );
385 System.out.println( "failed." );
388 System.out.print( "Methods on external nodes: " );
389 if ( Test.testExternalNodeRelatedMethods() ) {
390 System.out.println( "OK." );
394 System.out.println( "failed." );
397 System.out.print( "Deletion of external nodes: " );
398 if ( Test.testDeletionOfExternalNodes() ) {
399 System.out.println( "OK." );
403 System.out.println( "failed." );
406 System.out.print( "Subtree deletion: " );
407 if ( Test.testSubtreeDeletion() ) {
408 System.out.println( "OK." );
412 System.out.println( "failed." );
415 System.out.print( "Phylogeny branch: " );
416 if ( Test.testPhylogenyBranch() ) {
417 System.out.println( "OK." );
421 System.out.println( "failed." );
424 System.out.print( "Rerooting: " );
425 if ( Test.testRerooting() ) {
426 System.out.println( "OK." );
430 System.out.println( "failed." );
433 System.out.print( "Mipoint rooting: " );
434 if ( Test.testMidpointrooting() ) {
435 System.out.println( "OK." );
439 System.out.println( "failed." );
442 System.out.print( "Support count: " );
443 if ( Test.testSupportCount() ) {
444 System.out.println( "OK." );
448 System.out.println( "failed." );
451 System.out.print( "Support transfer: " );
452 if ( Test.testSupportTransfer() ) {
453 System.out.println( "OK." );
457 System.out.println( "failed." );
460 System.out.print( "Finding of LCA: " );
461 if ( Test.testGetLCA() ) {
462 System.out.println( "OK." );
466 System.out.println( "failed." );
469 System.out.print( "Calculation of distance between nodes: " );
470 if ( Test.testGetDistance() ) {
471 System.out.println( "OK." );
475 System.out.println( "failed." );
478 System.out.print( "SDIse: " );
479 if ( Test.testSDIse() ) {
480 System.out.println( "OK." );
484 System.out.println( "failed." );
487 System.out.print( "Taxonomy assigner: " );
488 if ( Test.testTaxonomyAssigner() ) {
489 System.out.println( "OK." );
493 System.out.println( "failed." );
496 System.out.print( "SDIunrooted: " );
497 if ( Test.testSDIunrooted() ) {
498 System.out.println( "OK." );
502 System.out.println( "failed." );
505 System.out.print( "GSDI: " );
506 if ( TestGSDI.test() ) {
507 System.out.println( "OK." );
511 System.out.println( "failed." );
514 System.out.print( "Descriptive statistics: " );
515 if ( Test.testDescriptiveStatistics() ) {
516 System.out.println( "OK." );
520 System.out.println( "failed." );
523 System.out.print( "Data objects and methods: " );
524 if ( Test.testDataObjects() ) {
525 System.out.println( "OK." );
529 System.out.println( "failed." );
532 System.out.print( "Properties map: " );
533 if ( Test.testPropertiesMap() ) {
534 System.out.println( "OK." );
538 System.out.println( "failed." );
541 System.out.print( "Phylogeny reconstruction:" );
542 System.out.println();
543 if ( TestPhylogenyReconstruction.test( new File( PATH_TO_TEST_DATA ) ) ) {
544 System.out.println( "OK." );
548 System.out.println( "failed." );
551 System.out.print( "Analysis of domain architectures: " );
552 System.out.println();
553 if ( TestSurfacing.test( new File( PATH_TO_TEST_DATA ) ) ) {
554 System.out.println( "OK." );
558 System.out.println( "failed." );
561 System.out.print( "GO: " );
562 System.out.println();
563 if ( TestGo.test( new File( PATH_TO_TEST_DATA ) ) ) {
564 System.out.println( "OK." );
568 System.out.println( "failed." );
571 System.out.print( "Modeling tools: " );
572 if ( TestPccx.test() ) {
573 System.out.println( "OK." );
577 System.out.println( "failed." );
580 System.out.print( "Split Matrix strict: " );
581 if ( Test.testSplitStrict() ) {
582 System.out.println( "OK." );
586 System.out.println( "failed." );
589 System.out.print( "Split Matrix: " );
590 if ( Test.testSplit() ) {
591 System.out.println( "OK." );
595 System.out.println( "failed." );
598 System.out.print( "Confidence Assessor: " );
599 if ( Test.testConfidenceAssessor() ) {
600 System.out.println( "OK." );
604 System.out.println( "failed." );
607 System.out.print( "Basic table: " );
608 if ( Test.testBasicTable() ) {
609 System.out.println( "OK." );
613 System.out.println( "failed." );
616 System.out.print( "General table: " );
617 if ( Test.testGeneralTable() ) {
618 System.out.println( "OK." );
622 System.out.println( "failed." );
625 System.out.print( "Amino acid sequence: " );
626 if ( Test.testAminoAcidSequence() ) {
627 System.out.println( "OK." );
631 System.out.println( "failed." );
634 System.out.print( "General MSA parser: " );
635 if ( Test.testGeneralMsaParser() ) {
636 System.out.println( "OK." );
640 System.out.println( "failed." );
643 System.out.print( "Fasta parser for msa: " );
644 if ( Test.testFastaParser() ) {
645 System.out.println( "OK." );
649 System.out.println( "failed." );
652 System.out.print( "Creation of balanced phylogeny: " );
653 if ( Test.testCreateBalancedPhylogeny() ) {
654 System.out.println( "OK." );
658 System.out.println( "failed." );
661 System.out.print( "EMBL Entry Retrieval: " );
662 if ( Test.testEmblEntryRetrieval() ) {
663 System.out.println( "OK." );
667 System.out.println( "failed." );
670 System.out.print( "Uniprot Entry Retrieval: " );
671 if ( Test.testUniprotEntryRetrieval() ) {
672 System.out.println( "OK." );
676 System.out.println( "failed." );
679 System.out.print( "Uniprot Taxonomy Search: " );
680 if ( Test.testUniprotTaxonomySearch() ) {
681 System.out.println( "OK." );
685 System.out.println( "failed." );
688 if ( Mafft.isInstalled() ) {
689 System.out.print( "MAFFT (external program): " );
690 if ( Test.testMafft() ) {
691 System.out.println( "OK." );
695 System.out.println( "failed [will not count towards failed tests]" );
698 System.out.print( "Next nodes with collapsed: " );
699 if ( Test.testNextNodeWithCollapsing() ) {
700 System.out.println( "OK." );
704 System.out.println( "failed." );
707 // System.out.print( "WABI TxSearch: " );
708 // if ( Test.testWabiTxSearch() ) {
709 // System.out.println( "OK." );
714 // .println( "failed [will not count towards failed tests since it might be due to absence internet connection]" );
716 System.out.println();
717 final Runtime rt = java.lang.Runtime.getRuntime();
718 final long free_memory = rt.freeMemory() / 1000000;
719 final long total_memory = rt.totalMemory() / 1000000;
720 System.out.println( "Running time : " + ( new Date().getTime() - start_time ) + "ms " + "(free memory: "
721 + free_memory + "MB, total memory: " + total_memory + "MB)" );
722 System.out.println();
723 System.out.println( "Successful tests: " + succeeded );
724 System.out.println( "Failed tests: " + failed );
725 System.out.println();
727 System.out.println( "OK." );
730 System.out.println( "Not OK." );
732 // System.out.println();
733 // Development.setTime( true );
735 // final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
736 // final String clc = System.getProperty( "user.dir" ) + ForesterUtil.getFileSeparator()
737 // + "examples" + ForesterUtil.getFileSeparator() + "CLC.nhx";
738 // final String multi = Test.PATH_TO_EXAMPLE_FILES +
739 // "multifurcations_ex_1.nhx";
740 // final String domains = Test.PATH_TO_EXAMPLE_FILES + "domains1.nhx";
741 // final Phylogeny t1 = factory.create( new File( domains ), new
742 // NHXParser() )[ 0 ];
743 // final Phylogeny t2 = factory.create( new File( clc ), new NHXParser() )[ 0 ];
745 // catch ( final Exception e ) {
746 // e.printStackTrace();
748 // t1.getRoot().preorderPrint();
749 // final PhylogenyFactory factory = ParserBasedPhylogenyFactory
753 // Helper.readNHtree( new File( PATH_TO_EXAMPLE_FILES
754 // + "\\AtNBSpos.nhx" ) );
756 // new File( PATH_TO_EXAMPLE_FILES + "\\AtNBSpos.nhx" ),
757 // new NHXParser() );
758 // Helper.readNHtree( new File( PATH_TO_EXAMPLE_FILES
759 // + "\\AtNBSpos.nhx" ) );
761 // new File( PATH_TO_EXAMPLE_FILES + "\\AtNBSpos.nhx" ),
762 // new NHXParser() );
765 // Helper.readNHtree( new File( PATH_TO_EXAMPLE_FILES
766 // + "\\big_tree.nhx" ) );
767 // Helper.readNHtree( new File( PATH_TO_EXAMPLE_FILES
768 // + "\\big_tree.nhx" ) );
770 // new File( PATH_TO_EXAMPLE_FILES + "\\big_tree.nhx" ),
771 // new NHXParser() );
773 // new File( PATH_TO_EXAMPLE_FILES + "\\big_tree.nhx" ),
774 // new NHXParser() );
776 // Helper.readNHtree( new File( PATH_TO_EXAMPLE_FILES
777 // + "\\big_tree.nhx" ) );
778 // Helper.readNHtree( new File( PATH_TO_EXAMPLE_FILES
779 // + "\\big_tree.nhx" ) );
782 // new File( PATH_TO_EXAMPLE_FILES + "\\big_tree.nhx" ),
783 // new NHXParser() );
785 // new File( PATH_TO_EXAMPLE_FILES + "\\big_tree.nhx" ),
786 // new NHXParser() );
788 // Helper.readNHtree( new File( PATH_TO_EXAMPLE_FILES
789 // + "\\AtNBSpos.nhx" ) );
791 // new File( PATH_TO_EXAMPLE_FILES + "\\AtNBSpos.nhx" ),
792 // new NHXParser() );
795 // catch ( IOException e ) {
796 // // TODO Auto-generated catch block
797 // e.printStackTrace();
801 private static boolean testBasicNodeMethods() {
803 if ( PhylogenyNode.getNodeCount() != 0 ) {
806 final PhylogenyNode n1 = new PhylogenyNode();
807 final PhylogenyNode n2 = PhylogenyNode
808 .createInstanceFromNhxString( "", PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
809 final PhylogenyNode n3 = PhylogenyNode
810 .createInstanceFromNhxString( "n3", PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
811 final PhylogenyNode n4 = PhylogenyNode
812 .createInstanceFromNhxString( "n4:0.01", PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
813 if ( n1.isHasAssignedEvent() ) {
816 if ( PhylogenyNode.getNodeCount() != 4 ) {
819 if ( n3.getIndicator() != 0 ) {
822 if ( n3.getNumberOfExternalNodes() != 1 ) {
825 if ( !n3.isExternal() ) {
828 if ( !n3.isRoot() ) {
831 if ( !n4.getName().equals( "n4" ) ) {
835 catch ( final Exception e ) {
836 e.printStackTrace( System.out );
842 private static boolean testBasicPhyloXMLparsing() {
844 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
845 final PhyloXmlParser xml_parser = new PhyloXmlParser();
846 final Phylogeny[] phylogenies_0 = factory.create( Test.PATH_TO_TEST_DATA + "phyloxml_test_t1.xml",
848 if ( xml_parser.getErrorCount() > 0 ) {
849 System.out.println( xml_parser.getErrorMessages().toString() );
852 if ( phylogenies_0.length != 4 ) {
855 final Phylogeny t1 = phylogenies_0[ 0 ];
856 final Phylogeny t2 = phylogenies_0[ 1 ];
857 final Phylogeny t3 = phylogenies_0[ 2 ];
858 final Phylogeny t4 = phylogenies_0[ 3 ];
859 if ( t1.getNumberOfExternalNodes() != 1 ) {
862 if ( !t1.isRooted() ) {
865 if ( t1.isRerootable() ) {
868 if ( !t1.getType().equals( "gene_tree" ) ) {
871 if ( t2.getNumberOfExternalNodes() != 2 ) {
874 if ( !isEqual( t2.getNode( "node a" ).getDistanceToParent(), 1.0 ) ) {
877 if ( !isEqual( t2.getNode( "node b" ).getDistanceToParent(), 2.0 ) ) {
880 if ( t2.getNode( "node a" ).getNodeData().getTaxonomies().size() != 2 ) {
883 if ( !t2.getNode( "node a" ).getNodeData().getTaxonomy( 0 ).getCommonName().equals( "some parasite" ) ) {
886 if ( !t2.getNode( "node a" ).getNodeData().getTaxonomy( 1 ).getCommonName().equals( "the host" ) ) {
889 if ( t2.getNode( "node a" ).getNodeData().getSequences().size() != 2 ) {
892 if ( !t2.getNode( "node a" ).getNodeData().getSequence( 0 ).getMolecularSequence()
893 .startsWith( "actgtgggggt" ) ) {
896 if ( !t2.getNode( "node a" ).getNodeData().getSequence( 1 ).getMolecularSequence()
897 .startsWith( "ctgtgatgcat" ) ) {
900 if ( t3.getNumberOfExternalNodes() != 4 ) {
903 if ( !t1.getName().equals( "t1" ) ) {
906 if ( !t2.getName().equals( "t2" ) ) {
909 if ( !t3.getName().equals( "t3" ) ) {
912 if ( !t4.getName().equals( "t4" ) ) {
915 if ( !t3.getIdentifier().getValue().equals( "1-1" ) ) {
918 if ( !t3.getIdentifier().getProvider().equals( "treebank" ) ) {
921 if ( !t3.getNode( "root node" ).getNodeData().getSequence().getType().equals( "protein" ) ) {
924 if ( !t3.getNode( "root node" ).getNodeData().getSequence().getName()
925 .equals( "Apoptosis facilitator Bcl-2-like 14 protein" ) ) {
928 if ( !t3.getNode( "root node" ).getNodeData().getSequence().getSymbol().equals( "BCL2L14" ) ) {
931 if ( !t3.getNode( "root node" ).getNodeData().getSequence().getAccession().getValue().equals( "Q9BZR8" ) ) {
934 if ( !t3.getNode( "root node" ).getNodeData().getSequence().getAccession().getSource().equals( "UniProtKB" ) ) {
937 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getDesc()
938 .equals( "apoptosis" ) ) {
941 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getRef()
942 .equals( "GO:0006915" ) ) {
945 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getSource()
946 .equals( "UniProtKB" ) ) {
949 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getEvidence()
950 .equals( "experimental" ) ) {
953 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getType()
954 .equals( "function" ) ) {
957 if ( ( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getConfidence()
961 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getConfidence()
962 .getType().equals( "ml" ) ) {
965 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getDesc()
966 .equals( "apoptosis" ) ) {
969 if ( ( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getProperties()
970 .getProperty( "AFFY:expression" ).getAppliesTo() != AppliesTo.ANNOTATION ) {
973 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getProperties()
974 .getProperty( "AFFY:expression" ).getDataType().equals( "xsd:double" ) ) {
977 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getProperties()
978 .getProperty( "AFFY:expression" ).getRef().equals( "AFFY:expression" ) ) {
981 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getProperties()
982 .getProperty( "AFFY:expression" ).getUnit().equals( "AFFY:x" ) ) {
985 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getProperties()
986 .getProperty( "AFFY:expression" ).getValue().equals( "0.2" ) ) {
989 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getProperties()
990 .getProperty( "MED:disease" ).getValue().equals( "lymphoma" ) ) {
993 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 0 ) ).getRef()
994 .equals( "GO:0005829" ) ) {
997 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getDesc()
998 .equals( "intracellular organelle" ) ) {
1001 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getUri( 0 ).getType().equals( "source" ) ) ) {
1004 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getUri( 0 ).getDescription()
1005 .equals( "UniProt link" ) ) ) {
1008 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getLocation().equals( "12p13-p12" ) ) ) {
1011 //if ( !( t3.getNode( "root node" ).getNodeData().getDistribution().getDesc().equals( "irgendwo" ) ) ) {
1014 // if ( !( t3.getNode( "root node" ).getNodeData().getReference().getDoi().equals( "10.1074/jbc.M005889200" ) ) ) {
1017 // if ( !t3.getNode( "root node" ).getNodeData().getTaxonomy().getType().equals( "host" ) ) {
1020 // if ( !t3.getNode( "root node" ).getNodeData().getTaxonomy().getTaxonomyCode().equals( "ECDYS" ) ) {
1023 // if ( !t3.getNode( "root node" ).getNodeData().getTaxonomy().getScientificName().equals( "ecdysozoa" ) ) {
1026 // if ( !t3.getNode( "root node" ).getNodeData().getTaxonomy().getCommonName().equals( "molting animals" ) ) {
1029 // if ( !t3.getNode( "root node" ).getNodeData().getTaxonomy().getIdentifier().getValue().equals( "1" ) ) {
1032 // if ( !t3.getNode( "root node" ).getNodeData().getTaxonomy().getIdentifier().getType().equals( "ncbi" ) ) {
1035 // if ( t3.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getTotalLength() != 124 ) {
1038 // if ( !t3.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 ).getName()
1039 // .equals( "B" ) ) {
1042 // if ( t3.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 ).getFrom() != 21 ) {
1045 // if ( t3.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 ).getTo() != 44 ) {
1048 // if ( t3.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 ).getLength() != 24 ) {
1051 // if ( t3.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 )
1052 // .getConfidence() != 2144 ) {
1055 // if ( !t3.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 ).getId()
1056 // .equals( "pfam" ) ) {
1059 // if ( t3.getNode( "node bb" ).getNodeData().getBinaryCharacters().getGainedCharacters().size() != 3 ) {
1062 // if ( t3.getNode( "node bb" ).getNodeData().getBinaryCharacters().getPresentCharacters().size() != 2 ) {
1065 // if ( t3.getNode( "node bb" ).getNodeData().getBinaryCharacters().getLostCharacters().size() != 1 ) {
1068 // if ( !t3.getNode( "node bb" ).getNodeData().getBinaryCharacters().getType().equals( "domains" ) ) {
1071 // if ( ( ( BinaryCharacters ) t3.getNode( "node bb" ).getNodeData().getBinaryCharacters().copy() )
1072 // .getLostCount() != BinaryCharacters.COUNT_DEFAULT ) {
1076 // if ( t3.getNode( "node b" ).getNodeData().getBinaryCharacters().getGainedCount() != 1 ) {
1079 // if ( t3.getNode( "node b" ).getNodeData().getBinaryCharacters().getGainedCharacters().size() != 1 ) {
1082 // if ( t3.getNode( "node b" ).getNodeData().getBinaryCharacters().getLostCount() != 3 ) {
1085 // if ( t3.getNode( "node b" ).getNodeData().getBinaryCharacters().getLostCharacters().size() != 3 ) {
1088 // if ( t3.getNode( "node b" ).getNodeData().getBinaryCharacters().getPresentCount() != 2 ) {
1091 // if ( t3.getNode( "node b" ).getNodeData().getBinaryCharacters().getPresentCharacters().size() != 2 ) {
1094 // if ( !t3.getNode( "node b" ).getNodeData().getBinaryCharacters().getType().equals( "characters" ) ) {
1097 // final Phylogeny[] phylogenies_1 = factory.create( Test.PATH_TO_TEST_DATA + "phyloxml_test_t4.xml",
1099 // if ( xml_parser.getErrorCount() > 0 ) {
1100 // System.out.println( xml_parser.getErrorMessages().toString() );
1103 // if ( phylogenies_1.length != 2 ) {
1106 // final Phylogeny a = phylogenies_1[ 0 ];
1107 // if ( !a.getName().equals( "tree 4" ) ) {
1110 // if ( a.getNumberOfExternalNodes() != 3 ) {
1113 // if ( !a.getNode( "node b1" ).getNodeData().getSequence().getName().equals( "b1 gene" ) ) {
1116 // if ( !a.getNode( "node b1" ).getNodeData().getTaxonomy().getCommonName().equals( "b1 species" ) ) {
1120 catch ( final Exception e ) {
1121 e.printStackTrace( System.out );
1127 private static boolean testBasicPhyloXMLparsingRoundtrip() {
1129 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
1130 final PhyloXmlParser xml_parser = new PhyloXmlParser();
1131 if ( USE_LOCAL_PHYLOXML_SCHEMA ) {
1132 xml_parser.setValidateAgainstSchema( PHYLOXML_LOCAL_XSD );
1135 xml_parser.setValidateAgainstSchema( PHYLOXML_REMOTE_XSD );
1137 final Phylogeny[] phylogenies_0 = factory.create( Test.PATH_TO_TEST_DATA + "phyloxml_test_t1.xml",
1139 if ( xml_parser.getErrorCount() > 0 ) {
1140 System.out.println( xml_parser.getErrorMessages().toString() );
1143 if ( phylogenies_0.length != 4 ) {
1146 final StringBuffer t1_sb = new StringBuffer( phylogenies_0[ 0 ].toPhyloXML( 0 ) );
1147 final Phylogeny[] phylogenies_t1 = factory.create( t1_sb, xml_parser );
1148 if ( phylogenies_t1.length != 1 ) {
1151 final Phylogeny t1_rt = phylogenies_t1[ 0 ];
1152 if ( !t1_rt.getDistanceUnit().equals( "cc" ) ) {
1155 if ( !t1_rt.isRooted() ) {
1158 if ( t1_rt.isRerootable() ) {
1161 if ( !t1_rt.getType().equals( "gene_tree" ) ) {
1164 final StringBuffer t2_sb = new StringBuffer( phylogenies_0[ 1 ].toPhyloXML( 0 ) );
1165 final Phylogeny[] phylogenies_t2 = factory.create( t2_sb, xml_parser );
1166 final Phylogeny t2_rt = phylogenies_t2[ 0 ];
1167 if ( t2_rt.getNode( "node a" ).getNodeData().getTaxonomies().size() != 2 ) {
1170 if ( !t2_rt.getNode( "node a" ).getNodeData().getTaxonomy( 0 ).getCommonName().equals( "some parasite" ) ) {
1173 if ( !t2_rt.getNode( "node a" ).getNodeData().getTaxonomy( 1 ).getCommonName().equals( "the host" ) ) {
1176 if ( t2_rt.getNode( "node a" ).getNodeData().getSequences().size() != 2 ) {
1179 if ( !t2_rt.getNode( "node a" ).getNodeData().getSequence( 0 ).getMolecularSequence()
1180 .startsWith( "actgtgggggt" ) ) {
1183 if ( !t2_rt.getNode( "node a" ).getNodeData().getSequence( 1 ).getMolecularSequence()
1184 .startsWith( "ctgtgatgcat" ) ) {
1187 final StringBuffer t3_sb_0 = new StringBuffer( phylogenies_0[ 2 ].toPhyloXML( 0 ) );
1188 final Phylogeny[] phylogenies_1_0 = factory.create( t3_sb_0, xml_parser );
1189 final StringBuffer t3_sb = new StringBuffer( phylogenies_1_0[ 0 ].toPhyloXML( 0 ) );
1190 final Phylogeny[] phylogenies_1 = factory.create( t3_sb, xml_parser );
1191 if ( phylogenies_1.length != 1 ) {
1194 final Phylogeny t3_rt = phylogenies_1[ 0 ];
1195 if ( !t3_rt.getName().equals( "t3" ) ) {
1198 if ( t3_rt.getNumberOfExternalNodes() != 4 ) {
1201 if ( !t3_rt.getIdentifier().getValue().equals( "1-1" ) ) {
1204 if ( !t3_rt.getIdentifier().getProvider().equals( "treebank" ) ) {
1207 if ( !t3_rt.getNode( "root node" ).getNodeData().getSequence().getType().equals( "protein" ) ) {
1210 if ( !t3_rt.getNode( "root node" ).getNodeData().getSequence().getName()
1211 .equals( "Apoptosis facilitator Bcl-2-like 14 protein" ) ) {
1214 if ( !t3_rt.getNode( "root node" ).getNodeData().getSequence().getSymbol().equals( "BCL2L14" ) ) {
1217 if ( !t3_rt.getNode( "root node" ).getNodeData().getSequence().getAccession().getValue().equals( "Q9BZR8" ) ) {
1220 if ( !t3_rt.getNode( "root node" ).getNodeData().getSequence().getAccession().getSource()
1221 .equals( "UniProtKB" ) ) {
1224 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getDesc()
1225 .equals( "apoptosis" ) ) {
1228 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getRef()
1229 .equals( "GO:0006915" ) ) {
1232 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getSource()
1233 .equals( "UniProtKB" ) ) {
1236 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getEvidence()
1237 .equals( "experimental" ) ) {
1240 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getType()
1241 .equals( "function" ) ) {
1244 if ( ( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getConfidence()
1245 .getValue() != 1 ) {
1248 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getConfidence()
1249 .getType().equals( "ml" ) ) {
1252 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getDesc()
1253 .equals( "apoptosis" ) ) {
1256 if ( ( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getProperties()
1257 .getProperty( "AFFY:expression" ).getAppliesTo() != AppliesTo.ANNOTATION ) {
1260 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getProperties()
1261 .getProperty( "AFFY:expression" ).getDataType().equals( "xsd:double" ) ) {
1264 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getProperties()
1265 .getProperty( "AFFY:expression" ).getRef().equals( "AFFY:expression" ) ) {
1268 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getProperties()
1269 .getProperty( "AFFY:expression" ).getUnit().equals( "AFFY:x" ) ) {
1272 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getProperties()
1273 .getProperty( "AFFY:expression" ).getValue().equals( "0.2" ) ) {
1276 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getProperties()
1277 .getProperty( "MED:disease" ).getValue().equals( "lymphoma" ) ) {
1280 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 0 ) ).getRef()
1281 .equals( "GO:0005829" ) ) {
1284 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getDesc()
1285 .equals( "intracellular organelle" ) ) {
1288 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getUri( 0 ).getType().equals( "source" ) ) ) {
1291 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getUri( 0 ).getDescription()
1292 .equals( "UniProt link" ) ) ) {
1295 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getLocation().equals( "12p13-p12" ) ) ) {
1298 if ( !( t3_rt.getNode( "root node" ).getNodeData().getReference().getDoi().equals( "10.1038/387489a0" ) ) ) {
1301 if ( !( t3_rt.getNode( "root node" ).getNodeData().getReference().getDescription()
1302 .equals( "Aguinaldo, A. M. A.; J. M. Turbeville, L. S. Linford, M. C. Rivera, J. R. Garey, R. A. Raff, & J. A. Lake (1997). \"Evidence for a clade of nematodes, arthropods and other moulting animals\". Nature 387 (6632): 489–493." ) ) ) {
1305 if ( !t3_rt.getNode( "root node" ).getNodeData().getTaxonomy().getTaxonomyCode().equals( "ECDYS" ) ) {
1308 if ( !t3_rt.getNode( "root node" ).getNodeData().getTaxonomy().getScientificName().equals( "ecdysozoa" ) ) {
1311 if ( !t3_rt.getNode( "root node" ).getNodeData().getTaxonomy().getCommonName().equals( "molting animals" ) ) {
1314 if ( !t3_rt.getNode( "root node" ).getNodeData().getTaxonomy().getIdentifier().getValue().equals( "1" ) ) {
1317 if ( !t3_rt.getNode( "root node" ).getNodeData().getTaxonomy().getIdentifier().getProvider()
1318 .equals( "ncbi" ) ) {
1321 if ( t3_rt.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getTotalLength() != 124 ) {
1324 if ( !t3_rt.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 )
1325 .getName().equals( "B" ) ) {
1328 if ( t3_rt.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 )
1329 .getFrom() != 21 ) {
1332 if ( t3_rt.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 ).getTo() != 44 ) {
1335 if ( t3_rt.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 )
1336 .getLength() != 24 ) {
1339 if ( t3_rt.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 )
1340 .getConfidence() != 2144 ) {
1343 if ( !t3_rt.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 ).getId()
1344 .equals( "pfam" ) ) {
1347 if ( t3_rt.getNode( "node bb" ).getNodeData().getBinaryCharacters().getGainedCharacters().size() != 3 ) {
1350 if ( t3_rt.getNode( "node bb" ).getNodeData().getBinaryCharacters().getPresentCharacters().size() != 2 ) {
1353 if ( t3_rt.getNode( "node bb" ).getNodeData().getBinaryCharacters().getLostCharacters().size() != 1 ) {
1356 if ( !t3_rt.getNode( "node bb" ).getNodeData().getBinaryCharacters().getType().equals( "domains" ) ) {
1359 final Taxonomy taxbb = t3_rt.getNode( "node bb" ).getNodeData().getTaxonomy();
1360 if ( !taxbb.getAuthority().equals( "Stephenson, 1935" ) ) {
1363 if ( !taxbb.getCommonName().equals( "starlet sea anemone" ) ) {
1366 if ( !taxbb.getIdentifier().getProvider().equals( "EOL" ) ) {
1369 if ( !taxbb.getIdentifier().getValue().equals( "704294" ) ) {
1372 if ( !taxbb.getTaxonomyCode().equals( "NEMVE" ) ) {
1375 if ( !taxbb.getScientificName().equals( "Nematostella vectensis" ) ) {
1378 if ( taxbb.getSynonyms().size() != 2 ) {
1381 if ( !taxbb.getSynonyms().contains( "Nematostella vectensis Stephenson1935" ) ) {
1384 if ( !taxbb.getSynonyms().contains( "See Anemone" ) ) {
1387 if ( !taxbb.getUri( 0 ).getDescription().equals( "EOL" ) ) {
1390 if ( !taxbb.getUri( 0 ).getType().equals( "linkout" ) ) {
1393 if ( !taxbb.getUri( 0 ).getValue().toString().equals( "http://www.eol.org/pages/704294" ) ) {
1396 if ( ( ( BinaryCharacters ) t3_rt.getNode( "node bb" ).getNodeData().getBinaryCharacters().copy() )
1397 .getLostCount() != BinaryCharacters.COUNT_DEFAULT ) {
1401 if ( t3_rt.getNode( "node b" ).getNodeData().getBinaryCharacters().getGainedCount() != 1 ) {
1404 if ( t3_rt.getNode( "node b" ).getNodeData().getBinaryCharacters().getGainedCharacters().size() != 1 ) {
1407 if ( t3_rt.getNode( "node b" ).getNodeData().getBinaryCharacters().getLostCount() != 3 ) {
1410 if ( t3_rt.getNode( "node b" ).getNodeData().getBinaryCharacters().getLostCharacters().size() != 3 ) {
1413 if ( t3_rt.getNode( "node b" ).getNodeData().getBinaryCharacters().getPresentCount() != 2 ) {
1416 if ( t3_rt.getNode( "node b" ).getNodeData().getBinaryCharacters().getPresentCharacters().size() != 2 ) {
1419 if ( !t3_rt.getNode( "node b" ).getNodeData().getBinaryCharacters().getType().equals( "characters" ) ) {
1423 if ( !t3_rt.getNode( "node ba" ).getNodeData().getDate().getDesc().equals( "Silurian" ) ) {
1426 if ( !t3_rt.getNode( "node ba" ).getNodeData().getDate().getValue().toPlainString()
1427 .equalsIgnoreCase( "435" ) ) {
1430 if ( !t3_rt.getNode( "node ba" ).getNodeData().getDate().getMin().toPlainString().equalsIgnoreCase( "416" ) ) {
1433 if ( !t3_rt.getNode( "node ba" ).getNodeData().getDate().getMax().toPlainString()
1434 .equalsIgnoreCase( "443.7" ) ) {
1437 if ( !t3_rt.getNode( "node ba" ).getNodeData().getDate().getUnit().equals( "mya" ) ) {
1440 if ( !t3_rt.getNode( "node bb" ).getNodeData().getDate().getDesc().equals( "Triassic" ) ) {
1443 if ( !t3_rt.getNode( "node bc" ).getNodeData().getDate().getValue().toPlainString()
1444 .equalsIgnoreCase( "433" ) ) {
1448 catch ( final Exception e ) {
1449 e.printStackTrace( System.out );
1455 private static boolean testBasicPhyloXMLparsingValidating() {
1457 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
1458 PhyloXmlParser xml_parser = null;
1460 xml_parser = PhyloXmlParser.createPhyloXmlParserXsdValidating();
1462 catch ( final Exception e ) {
1463 // Do nothing -- means were not running from jar.
1465 if ( xml_parser == null ) {
1466 xml_parser = new PhyloXmlParser();
1467 if ( USE_LOCAL_PHYLOXML_SCHEMA ) {
1468 xml_parser.setValidateAgainstSchema( PHYLOXML_LOCAL_XSD );
1471 xml_parser.setValidateAgainstSchema( PHYLOXML_REMOTE_XSD );
1474 final Phylogeny[] phylogenies_0 = factory.create( Test.PATH_TO_TEST_DATA + "phyloxml_test_t1.xml",
1476 if ( xml_parser.getErrorCount() > 0 ) {
1477 System.out.println( xml_parser.getErrorMessages().toString() );
1480 if ( phylogenies_0.length != 4 ) {
1483 final Phylogeny t1 = phylogenies_0[ 0 ];
1484 final Phylogeny t2 = phylogenies_0[ 1 ];
1485 final Phylogeny t3 = phylogenies_0[ 2 ];
1486 final Phylogeny t4 = phylogenies_0[ 3 ];
1487 if ( !t1.getName().equals( "t1" ) ) {
1490 if ( !t2.getName().equals( "t2" ) ) {
1493 if ( !t3.getName().equals( "t3" ) ) {
1496 if ( !t4.getName().equals( "t4" ) ) {
1499 if ( t1.getNumberOfExternalNodes() != 1 ) {
1502 if ( t2.getNumberOfExternalNodes() != 2 ) {
1505 if ( t3.getNumberOfExternalNodes() != 4 ) {
1508 final String x2 = Test.PATH_TO_TEST_DATA + "phyloxml_test_t1.xml";
1509 final Phylogeny[] phylogenies_1 = factory.create( x2, xml_parser );
1510 if ( xml_parser.getErrorCount() > 0 ) {
1511 System.out.println( "errors:" );
1512 System.out.println( xml_parser.getErrorMessages().toString() );
1515 if ( phylogenies_1.length != 4 ) {
1518 final Phylogeny[] phylogenies_2 = factory.create( Test.PATH_TO_TEST_DATA + "phyloxml_test_t3.xml",
1520 if ( xml_parser.getErrorCount() > 0 ) {
1521 System.out.println( "errors:" );
1522 System.out.println( xml_parser.getErrorMessages().toString() );
1525 if ( phylogenies_2.length != 1 ) {
1528 if ( phylogenies_2[ 0 ].getNumberOfExternalNodes() != 2 ) {
1531 final Phylogeny[] phylogenies_3 = factory.create( Test.PATH_TO_TEST_DATA + "phyloxml_test_t4.xml",
1533 if ( xml_parser.getErrorCount() > 0 ) {
1534 System.out.println( xml_parser.getErrorMessages().toString() );
1537 if ( phylogenies_3.length != 2 ) {
1540 final Phylogeny a = phylogenies_3[ 0 ];
1541 if ( !a.getName().equals( "tree 4" ) ) {
1544 if ( a.getNumberOfExternalNodes() != 3 ) {
1547 if ( !a.getNode( "node b1" ).getNodeData().getSequence().getName().equals( "b1 gene" ) ) {
1550 if ( !a.getNode( "node b1" ).getNodeData().getTaxonomy().getCommonName().equals( "b1 species" ) ) {
1553 final Phylogeny[] phylogenies_4 = factory.create( Test.PATH_TO_TEST_DATA + "special_characters.xml",
1555 if ( xml_parser.getErrorCount() > 0 ) {
1556 System.out.println( xml_parser.getErrorMessages().toString() );
1559 if ( phylogenies_4.length != 1 ) {
1562 final Phylogeny s = phylogenies_4[ 0 ];
1563 if ( s.getNumberOfExternalNodes() != 6 ) {
1566 s.getNode( "first" );
1568 s.getNode( "\"<a'b&c'd\">\"" );
1569 s.getNode( "'''\"" );
1570 s.getNode( "\"\"\"" );
1571 s.getNode( "dick & doof" );
1573 catch ( final Exception e ) {
1574 e.printStackTrace( System.out );
1580 private static boolean testBasicTable() {
1582 final BasicTable<String> t0 = new BasicTable<String>();
1583 if ( t0.getNumberOfColumns() != 0 ) {
1586 if ( t0.getNumberOfRows() != 0 ) {
1589 t0.setValue( 3, 2, "23" );
1590 t0.setValue( 10, 1, "error" );
1591 t0.setValue( 10, 1, "110" );
1592 t0.setValue( 9, 1, "19" );
1593 t0.setValue( 1, 10, "101" );
1594 t0.setValue( 10, 10, "1010" );
1595 t0.setValue( 100, 10, "10100" );
1596 t0.setValue( 0, 0, "00" );
1597 if ( !t0.getValue( 3, 2 ).equals( "23" ) ) {
1600 if ( !t0.getValue( 10, 1 ).equals( "110" ) ) {
1603 if ( !t0.getValueAsString( 1, 10 ).equals( "101" ) ) {
1606 if ( !t0.getValueAsString( 10, 10 ).equals( "1010" ) ) {
1609 if ( !t0.getValueAsString( 100, 10 ).equals( "10100" ) ) {
1612 if ( !t0.getValueAsString( 9, 1 ).equals( "19" ) ) {
1615 if ( !t0.getValueAsString( 0, 0 ).equals( "00" ) ) {
1618 if ( t0.getNumberOfColumns() != 101 ) {
1621 if ( t0.getNumberOfRows() != 11 ) {
1624 if ( t0.getValueAsString( 49, 4 ) != null ) {
1627 final String l = ForesterUtil.getLineSeparator();
1628 final StringBuffer source = new StringBuffer();
1629 source.append( "" + l );
1630 source.append( "# 1 1 1 1 1 1 1 1" + l );
1631 source.append( " 00 01 02 03" + l );
1632 source.append( " 10 11 12 13 " + l );
1633 source.append( "20 21 22 23 " + l );
1634 source.append( " 30 31 32 33" + l );
1635 source.append( "40 41 42 43" + l );
1636 source.append( " # 1 1 1 1 1 " + l );
1637 source.append( "50 51 52 53 54" + l );
1638 final BasicTable<String> t1 = BasicTableParser.parse( source.toString(), " " );
1639 if ( t1.getNumberOfColumns() != 5 ) {
1642 if ( t1.getNumberOfRows() != 6 ) {
1645 if ( !t1.getValueAsString( 0, 0 ).equals( "00" ) ) {
1648 if ( !t1.getValueAsString( 1, 0 ).equals( "01" ) ) {
1651 if ( !t1.getValueAsString( 3, 0 ).equals( "03" ) ) {
1654 if ( !t1.getValueAsString( 4, 5 ).equals( "54" ) ) {
1657 final StringBuffer source1 = new StringBuffer();
1658 source1.append( "" + l );
1659 source1.append( "# 1; 1; 1; 1 ;1 ;1; 1 ;1;" + l );
1660 source1.append( " 00; 01 ;02;03" + l );
1661 source1.append( " 10; 11; 12; 13 " + l );
1662 source1.append( "20; 21; 22; 23 " + l );
1663 source1.append( " 30; 31; 32; 33" + l );
1664 source1.append( "40;41;42;43" + l );
1665 source1.append( " # 1 1 1 1 1 " + l );
1666 source1.append( ";;;50 ; ;52; 53;;54 " + l );
1667 final BasicTable<String> t2 = BasicTableParser.parse( source1.toString(), ";" );
1668 if ( t2.getNumberOfColumns() != 5 ) {
1671 if ( t2.getNumberOfRows() != 6 ) {
1674 if ( !t2.getValueAsString( 0, 0 ).equals( "00" ) ) {
1677 if ( !t2.getValueAsString( 1, 0 ).equals( "01" ) ) {
1680 if ( !t2.getValueAsString( 3, 0 ).equals( "03" ) ) {
1683 if ( !t2.getValueAsString( 3, 3 ).equals( "33" ) ) {
1686 if ( !t2.getValueAsString( 3, 5 ).equals( "53" ) ) {
1689 if ( !t2.getValueAsString( 1, 5 ).equals( "" ) ) {
1692 final StringBuffer source2 = new StringBuffer();
1693 source2.append( "" + l );
1694 source2.append( "comment: 1; 1; 1; 1 ;1 ;1; 1 ;1;" + l );
1695 source2.append( " 00; 01 ;02;03" + l );
1696 source2.append( " 10; 11; 12; 13 " + l );
1697 source2.append( "20; 21; 22; 23 " + l );
1698 source2.append( " " + l );
1699 source2.append( " 30; 31; 32; 33" + l );
1700 source2.append( "40;41;42;43" + l );
1701 source2.append( " comment: 1 1 1 1 1 " + l );
1702 source2.append( ";;;50 ; 52; 53;;54 " + l );
1703 final List<BasicTable<String>> tl = BasicTableParser.parse( source2.toString(),
1708 if ( tl.size() != 2 ) {
1711 final BasicTable<String> t3 = tl.get( 0 );
1712 final BasicTable<String> t4 = tl.get( 1 );
1713 if ( t3.getNumberOfColumns() != 4 ) {
1716 if ( t3.getNumberOfRows() != 3 ) {
1719 if ( t4.getNumberOfColumns() != 4 ) {
1722 if ( t4.getNumberOfRows() != 3 ) {
1725 if ( !t3.getValueAsString( 0, 0 ).equals( "00" ) ) {
1728 if ( !t4.getValueAsString( 0, 0 ).equals( "30" ) ) {
1732 catch ( final Exception e ) {
1733 e.printStackTrace( System.out );
1739 private static boolean testBasicTolXMLparsing() {
1741 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
1742 final TolParser parser = new TolParser();
1743 final Phylogeny[] phylogenies_0 = factory.create( Test.PATH_TO_TEST_DATA + "tol_2484.tol", parser );
1744 if ( parser.getErrorCount() > 0 ) {
1745 System.out.println( parser.getErrorMessages().toString() );
1748 if ( phylogenies_0.length != 1 ) {
1751 final Phylogeny t1 = phylogenies_0[ 0 ];
1752 if ( t1.getNumberOfExternalNodes() != 5 ) {
1755 if ( !t1.isRooted() ) {
1758 if ( !t1.getRoot().getNodeData().getTaxonomy().getScientificName().equals( "Mesozoa" ) ) {
1761 if ( !t1.getRoot().getNodeData().getTaxonomy().getIdentifier().getValue().equals( "2484" ) ) {
1764 if ( !t1.getRoot().getChildNode( 0 ).getNodeData().getTaxonomy().getScientificName().equals( "Rhombozoa" ) ) {
1767 if ( t1.getRoot().getChildNode( 0 ).getNumberOfDescendants() != 3 ) {
1770 final Phylogeny[] phylogenies_1 = factory.create( Test.PATH_TO_TEST_DATA + "tol_2.tol", parser );
1771 if ( parser.getErrorCount() > 0 ) {
1772 System.out.println( parser.getErrorMessages().toString() );
1775 if ( phylogenies_1.length != 1 ) {
1778 final Phylogeny t2 = phylogenies_1[ 0 ];
1779 if ( t2.getNumberOfExternalNodes() != 664 ) {
1782 if ( !t2.isRooted() ) {
1785 if ( !t2.getRoot().getNodeData().getTaxonomy().getScientificName().equals( "Eubacteria" ) ) {
1788 if ( !t2.getRoot().getNodeData().getTaxonomy().getIdentifier().getValue().equals( "2" ) ) {
1791 if ( t2.getRoot().getNumberOfDescendants() != 24 ) {
1794 if ( t2.getRoot().getNumberOfDescendants() != 24 ) {
1797 if ( !t2.getRoot().getChildNode( 0 ).getNodeData().getTaxonomy().getScientificName().equals( "Aquificae" ) ) {
1800 if ( !t2.getRoot().getChildNode( 0 ).getChildNode( 0 ).getNodeData().getTaxonomy().getScientificName()
1801 .equals( "Aquifex" ) ) {
1804 final Phylogeny[] phylogenies_2 = factory.create( Test.PATH_TO_TEST_DATA + "tol_5.tol", parser );
1805 if ( parser.getErrorCount() > 0 ) {
1806 System.out.println( parser.getErrorMessages().toString() );
1809 if ( phylogenies_2.length != 1 ) {
1812 final Phylogeny t3 = phylogenies_2[ 0 ];
1813 if ( t3.getNumberOfExternalNodes() != 184 ) {
1816 if ( !t3.getRoot().getNodeData().getTaxonomy().getScientificName().equals( "Viruses" ) ) {
1819 if ( !t3.getRoot().getNodeData().getTaxonomy().getIdentifier().getValue().equals( "5" ) ) {
1822 if ( t3.getRoot().getNumberOfDescendants() != 6 ) {
1825 final Phylogeny[] phylogenies_3 = factory.create( Test.PATH_TO_TEST_DATA + "tol_4567.tol", parser );
1826 if ( parser.getErrorCount() > 0 ) {
1827 System.out.println( parser.getErrorMessages().toString() );
1830 if ( phylogenies_3.length != 1 ) {
1833 final Phylogeny t4 = phylogenies_3[ 0 ];
1834 if ( t4.getNumberOfExternalNodes() != 1 ) {
1837 if ( !t4.getRoot().getNodeData().getTaxonomy().getScientificName().equals( "Marpissa decorata" ) ) {
1840 if ( !t4.getRoot().getNodeData().getTaxonomy().getIdentifier().getValue().equals( "4567" ) ) {
1843 if ( t4.getRoot().getNumberOfDescendants() != 0 ) {
1846 final Phylogeny[] phylogenies_4 = factory.create( Test.PATH_TO_TEST_DATA + "tol_16299.tol", parser );
1847 if ( parser.getErrorCount() > 0 ) {
1848 System.out.println( parser.getErrorMessages().toString() );
1851 if ( phylogenies_4.length != 1 ) {
1854 final Phylogeny t5 = phylogenies_4[ 0 ];
1855 if ( t5.getNumberOfExternalNodes() != 13 ) {
1858 if ( !t5.getRoot().getNodeData().getTaxonomy().getScientificName().equals( "Hominidae" ) ) {
1861 if ( !t5.getRoot().getNodeData().getTaxonomy().getIdentifier().getValue().equals( "16299" ) ) {
1864 if ( t5.getRoot().getNumberOfDescendants() != 2 ) {
1868 catch ( final Exception e ) {
1869 e.printStackTrace( System.out );
1875 private static boolean testBasicTreeMethods() {
1877 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
1878 final Phylogeny t1 = factory.create();
1879 if ( !t1.isEmpty() ) {
1882 final Phylogeny t2 = factory.create( "((A:1,B:2)AB:1,(C:3,D:5)CD:3)ABCD:0.5", new NHXParser() )[ 0 ];
1883 if ( t2.getNumberOfExternalNodes() != 4 ) {
1886 if ( t2.getHeight() != 8.5 ) {
1889 if ( !t2.isCompletelyBinary() ) {
1892 if ( t2.isEmpty() ) {
1895 final Phylogeny t3 = factory.create( "((A:1,B:2,C:10)ABC:1,(D:3,E:5)DE:3)", new NHXParser() )[ 0 ];
1896 if ( t3.getNumberOfExternalNodes() != 5 ) {
1899 if ( t3.getHeight() != 11 ) {
1902 if ( t3.isCompletelyBinary() ) {
1905 final PhylogenyNode n = t3.getNode( "ABC" );
1906 PhylogenyNodeIterator it;
1907 for( it = n.iterateChildNodesForward(); it.hasNext(); ) {
1910 for( it.reset(); it.hasNext(); ) {
1913 final PhylogenyNodeIterator it2 = n.iterateChildNodesForward();
1914 if ( !it2.next().getName().equals( "A" ) ) {
1917 if ( !it2.next().getName().equals( "B" ) ) {
1920 if ( !it2.next().getName().equals( "C" ) ) {
1923 if ( it2.hasNext() ) {
1926 final Phylogeny t4 = factory.create( "((A:1,B:2,C:10)ABC:1,(D:3,E:5)DE:3,(F,G,H,I))", new NHXParser() )[ 0 ];
1927 if ( t4.getNumberOfExternalNodes() != 9 ) {
1930 if ( t4.getHeight() != 11 ) {
1933 if ( t4.isCompletelyBinary() ) {
1936 final StringBuffer sb5 = new StringBuffer( "(((A11:2)A1:2,(A21:1,A22:2,A23)A2:11,A3:2)A:2,B:10,C:3,D:8)" );
1937 final Phylogeny t5 = factory.create( sb5, new NHXParser() )[ 0 ];
1938 if ( t5.getNumberOfExternalNodes() != 8 ) {
1941 if ( t5.getHeight() != 15 ) {
1944 final StringBuffer sb6 = new StringBuffer( "(X,Y,Z,(((A111)A11:2)A1:2,(X,Y,Z,A21:1,A22:2,A23)A2:11,A3:2)A:2,B:10,C:3,D:8)" );
1945 final Phylogeny t6 = factory.create( sb6, new NHXParser() )[ 0 ];
1946 if ( t6.getHeight() != 15 ) {
1949 final StringBuffer sb7 = new StringBuffer( "(((A11:2)A1:2,(A21:1,A22:2,A23)A2:11,A3:2)A:2,B:10,C:15,D:8)" );
1950 final Phylogeny t7 = factory.create( sb7, new NHXParser() )[ 0 ];
1951 if ( t7.getHeight() != 15 ) {
1954 final StringBuffer sb8 = new StringBuffer( "(((A11:11)A1:2,(A21:2,A22:2,A23,A24,AA:)A2:11,A3:2)A:2,B:15,C:15,D:15)" );
1955 final Phylogeny t8 = factory.create( sb8, new NHXParser() )[ 0 ];
1956 if ( t8.getNumberOfExternalNodes() != 10 ) {
1959 if ( t8.getHeight() != 15 ) {
1962 final char[] a9 = new char[] {};
1963 final Phylogeny t9 = factory.create( a9, new NHXParser() )[ 0 ];
1964 if ( t9.getHeight() != 0 ) {
1967 final char[] a10 = new char[] { 'a', ':', '6' };
1968 final Phylogeny t10 = factory.create( a10, new NHXParser() )[ 0 ];
1969 if ( t10.getHeight() != 6 ) {
1973 catch ( final Exception e ) {
1974 e.printStackTrace( System.out );
1980 private static boolean testConfidenceAssessor() {
1982 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
1983 final Phylogeny t0 = factory.create( "((((A,B)ab,C)abc,D)abcd,E)abcde", new NHXParser() )[ 0 ];
1984 final Phylogeny[] ev0 = factory
1985 .create( "((((A,B),C),D),E);((((A,B),C),D),E);((((A,B),C),D),E);((((A,B),C),D),E);",
1987 ConfidenceAssessor.evaluate( "bootstrap", ev0, t0, false, 1, 0, 2 );
1988 if ( !isEqual( t0.getNode( "ab" ).getBranchData().getConfidence( 0 ).getValue(), 3 ) ) {
1991 if ( !isEqual( t0.getNode( "abc" ).getBranchData().getConfidence( 0 ).getValue(), 3 ) ) {
1994 final Phylogeny t1 = factory.create( "((((A,B)ab[&&NHX:B=50],C)abc,D)abcd,E)abcde", new NHXParser() )[ 0 ];
1995 final Phylogeny[] ev1 = factory
1996 .create( "((((A,B),C),D),E);((A,B),((E,D),C));(((A,B),C),(E,D));(A,(((E,D),C),B));(B,(A,((E,D),C)));(C,((E,D),(A,B)));(D,(E,((A,B),C)));",
1998 ConfidenceAssessor.evaluate( "bootstrap", ev1, t1, false, 1 );
1999 if ( !isEqual( t1.getNode( "ab" ).getBranchData().getConfidence( 1 ).getValue(), 7 ) ) {
2002 if ( !isEqual( t1.getNode( "abc" ).getBranchData().getConfidence( 0 ).getValue(), 7 ) ) {
2005 final Phylogeny t_b = factory.create( "((((A,C)ac,D)acd,E)acde,B)abcde", new NHXParser() )[ 0 ];
2006 final Phylogeny[] ev_b = factory
2007 .create( "((A,C),X);((A,X),C);(A,C);((((A,B),C),D),E);((A,B),((E,D),C));(((A,B),C),(E,D));(A,(((E,D),C),B));(B,(A,((E,D),C)));(C,((E,D),(A,B)));(D,(E,((A,B),C)));((((A,C)ac,D)acd,E)acde,B)abcd",
2009 ConfidenceAssessor.evaluate( "bootstrap", ev_b, t_b, false, 1 );
2010 // Archaeopteryx.createApplication( t_b ); //TODO use me again me working here...
2011 if ( !isEqual( t_b.getNode( "ac" ).getBranchData().getConfidence( 0 ).getValue(), 4 ) ) {
2014 if ( !isEqual( t_b.getNode( "acd" ).getBranchData().getConfidence( 0 ).getValue(), 1 ) ) {
2018 final Phylogeny t1x = factory.create( "((((A,B)ab,C)abc,D)abcd,E)abcde", new NHXParser() )[ 0 ];
2019 final Phylogeny[] ev1x = factory
2020 .create( "((((A,B),C),D),E);((A,B),((E,D),C));(((A,B),C),(E,D));(A,(((E,D),C),B));(B,(A,((E,D),C)));(C,((E,D),(A,B)));(D,(E,((A,B),C)));",
2022 ConfidenceAssessor.evaluate( "bootstrap", ev1x, t1x, true, 1 );
2023 if ( !isEqual( t1x.getNode( "ab" ).getBranchData().getConfidence( 0 ).getValue(), 7 ) ) {
2026 if ( !isEqual( t1x.getNode( "abc" ).getBranchData().getConfidence( 0 ).getValue(), 7 ) ) {
2029 final Phylogeny t_bx = factory.create( "((((A,C)ac,D)acd,E)acde,B)abcde", new NHXParser() )[ 0 ];
2030 final Phylogeny[] ev_bx = factory
2031 .create( "((((A,B),C),D),E);((A,B),((E,D),C));(((A,B),C),(E,D));(A,(((E,D),C),B));(B,(A,((E,D),C)));(C,((E,D),(A,B)));(D,(E,((A,B),C)));((((A,C)ac,D)acd,E)acde,B)abcd",
2033 ConfidenceAssessor.evaluate( "bootstrap", ev_bx, t_bx, true, 1 );
2034 if ( !isEqual( t_bx.getNode( "ac" ).getBranchData().getConfidence( 0 ).getValue(), 1 ) ) {
2037 if ( !isEqual( t_bx.getNode( "acd" ).getBranchData().getConfidence( 0 ).getValue(), 1 ) ) {
2041 final Phylogeny[] t2 = factory
2042 .create( "((((a,b),c),d),e);(((a,b),c),(d,e));(((((a,b),c),d),e),f);((((a,b),c),(d,e)),f);(((a,b),c),d,e);((a,b,c),d,e);",
2044 final Phylogeny[] ev2 = factory
2045 .create( "((((a,b),c),d),e);((((a,b),c),d),e);((((a,b),e),d),c);((((a,b),e),d),c);(((a,b),(c,d)),e);((a,b),x);((a,b),(x,y));(a,b);(a,e);(a,b,c);",
2047 for( final Phylogeny target : t2 ) {
2048 ConfidenceAssessor.evaluate( "bootstrap", ev2, target, false, 1 );
2051 final Phylogeny t4 = factory.create( "((((((A,B)ab,C)abc,D)abcd,E)abcde,F)abcdef,G)abcdefg",
2052 new NHXParser() )[ 0 ];
2053 final Phylogeny[] ev4 = factory.create( "(((A,B),C),(X,Y));((F,G),((A,B,C),(D,E)))", new NHXParser() );
2054 ConfidenceAssessor.evaluate( "bootstrap", ev4, t4, false, 1 );
2055 if ( !isEqual( t4.getNode( "ab" ).getBranchData().getConfidence( 0 ).getValue(), 1 ) ) {
2058 if ( !isEqual( t4.getNode( "abc" ).getBranchData().getConfidence( 0 ).getValue(), 2 ) ) {
2061 if ( !isEqual( t4.getNode( "abcde" ).getBranchData().getConfidence( 0 ).getValue(), 1 ) ) {
2065 catch ( final Exception e ) {
2066 e.printStackTrace();
2072 private static boolean testCopyOfNodeData() {
2074 final PhylogenyNode n1 = PhylogenyNode
2075 .createInstanceFromNhxString( "n5:0.1[&&NHX:S=Ecoli:E=1.1.1.1:D=Y:Co=Y:B=56:T=1:O=22:SO=33:SN=44:W=2:C=10.20.30:XN=S=tag1=value1=unit1]" );
2076 final PhylogenyNode n2 = n1.copyNodeData();
2077 if ( !n1.toNewHampshireX().equals( n2.toNewHampshireX() ) ) {
2081 catch ( final Exception e ) {
2082 e.printStackTrace();
2088 private static boolean testDataObjects() {
2090 final Confidence s0 = new Confidence();
2091 final Confidence s1 = new Confidence();
2092 if ( !s0.isEqual( s1 ) ) {
2095 final Confidence s2 = new Confidence( 0.23, "bootstrap" );
2096 final Confidence s3 = new Confidence( 0.23, "bootstrap" );
2097 if ( s2.isEqual( s1 ) ) {
2100 if ( !s2.isEqual( s3 ) ) {
2103 final Confidence s4 = ( Confidence ) s3.copy();
2104 if ( !s4.isEqual( s3 ) ) {
2111 final Taxonomy t1 = new Taxonomy();
2112 final Taxonomy t2 = new Taxonomy();
2113 final Taxonomy t3 = new Taxonomy();
2114 final Taxonomy t4 = new Taxonomy();
2115 final Taxonomy t5 = new Taxonomy();
2116 t1.setIdentifier( new Identifier( "ecoli" ) );
2117 t1.setTaxonomyCode( "ECOLI" );
2118 t1.setScientificName( "E. coli" );
2119 t1.setCommonName( "coli" );
2120 final Taxonomy t0 = ( Taxonomy ) t1.copy();
2121 if ( !t1.isEqual( t0 ) ) {
2124 t2.setIdentifier( new Identifier( "ecoli" ) );
2125 t2.setTaxonomyCode( "other" );
2126 t2.setScientificName( "what" );
2127 t2.setCommonName( "something" );
2128 if ( !t1.isEqual( t2 ) ) {
2131 t2.setIdentifier( new Identifier( "nemve" ) );
2132 if ( t1.isEqual( t2 ) ) {
2135 t1.setIdentifier( null );
2136 t3.setTaxonomyCode( "ECOLI" );
2137 t3.setScientificName( "what" );
2138 t3.setCommonName( "something" );
2139 if ( !t1.isEqual( t3 ) ) {
2142 t1.setIdentifier( null );
2143 t1.setTaxonomyCode( "" );
2144 t4.setScientificName( "E. ColI" );
2145 t4.setCommonName( "something" );
2146 if ( !t1.isEqual( t4 ) ) {
2149 t4.setScientificName( "B. subtilis" );
2150 t4.setCommonName( "something" );
2151 if ( t1.isEqual( t4 ) ) {
2154 t1.setIdentifier( null );
2155 t1.setTaxonomyCode( "" );
2156 t1.setScientificName( "" );
2157 t5.setCommonName( "COLI" );
2158 if ( !t1.isEqual( t5 ) ) {
2161 t5.setCommonName( "vibrio" );
2162 if ( t1.isEqual( t5 ) ) {
2167 final Identifier id0 = new Identifier( "123", "pfam" );
2168 final Identifier id1 = ( Identifier ) id0.copy();
2169 if ( !id1.isEqual( id1 ) ) {
2172 if ( !id1.isEqual( id0 ) ) {
2175 if ( !id0.isEqual( id1 ) ) {
2182 final ProteinDomain pd0 = new ProteinDomain( "abc", 100, 200 );
2183 final ProteinDomain pd1 = ( ProteinDomain ) pd0.copy();
2184 if ( !pd1.isEqual( pd1 ) ) {
2187 if ( !pd1.isEqual( pd0 ) ) {
2192 final ProteinDomain pd2 = new ProteinDomain( pd0.getName(), pd0.getFrom(), pd0.getTo(), "id" );
2193 final ProteinDomain pd3 = ( ProteinDomain ) pd2.copy();
2194 if ( !pd3.isEqual( pd3 ) ) {
2197 if ( !pd2.isEqual( pd3 ) ) {
2200 if ( !pd0.isEqual( pd3 ) ) {
2205 // DomainArchitecture
2206 // ------------------
2207 final ProteinDomain d0 = new ProteinDomain( "domain0", 10, 20 );
2208 final ProteinDomain d1 = new ProteinDomain( "domain1", 30, 40 );
2209 final ProteinDomain d2 = new ProteinDomain( "domain2", 50, 60 );
2210 final ProteinDomain d3 = new ProteinDomain( "domain3", 70, 80 );
2211 final ProteinDomain d4 = new ProteinDomain( "domain4", 90, 100 );
2212 final ArrayList<PhylogenyData> domains0 = new ArrayList<PhylogenyData>();
2217 final DomainArchitecture ds0 = new DomainArchitecture( domains0, 110 );
2218 if ( ds0.getNumberOfDomains() != 4 ) {
2221 final DomainArchitecture ds1 = ( DomainArchitecture ) ds0.copy();
2222 if ( !ds0.isEqual( ds0 ) ) {
2225 if ( !ds0.isEqual( ds1 ) ) {
2228 if ( ds1.getNumberOfDomains() != 4 ) {
2231 final ArrayList<PhylogenyData> domains1 = new ArrayList<PhylogenyData>();
2236 final DomainArchitecture ds2 = new DomainArchitecture( domains1, 200 );
2237 if ( ds0.isEqual( ds2 ) ) {
2243 final DomainArchitecture ds3 = new DomainArchitecture( "120>30>40>0.9>b>50>60>0.4>c>10>20>0.1>a" );
2244 if ( !ds3.toNHX().toString().equals( ":DS=120>10>20>0.1>a>30>40>0.9>b>50>60>0.4>c" ) ) {
2245 System.out.println( ds3.toNHX() );
2248 if ( ds3.getNumberOfDomains() != 3 ) {
2253 final Event e1 = new Event( Event.EventType.fusion );
2254 if ( e1.isDuplication() ) {
2257 if ( !e1.isFusion() ) {
2260 if ( !e1.asText().toString().equals( "fusion" ) ) {
2263 if ( !e1.asSimpleText().toString().equals( "fusion" ) ) {
2266 final Event e11 = new Event( Event.EventType.fusion );
2267 if ( !e11.isEqual( e1 ) ) {
2270 if ( !e11.toNHX().toString().equals( "" ) ) {
2273 final Event e2 = new Event( Event.EventType.speciation_or_duplication );
2274 if ( e2.isDuplication() ) {
2277 if ( !e2.isSpeciationOrDuplication() ) {
2280 if ( !e2.asText().toString().equals( "speciation_or_duplication" ) ) {
2283 if ( !e2.asSimpleText().toString().equals( "?" ) ) {
2286 if ( !e2.toNHX().toString().equals( ":D=?" ) ) {
2289 if ( e11.isEqual( e2 ) ) {
2292 final Event e2c = ( Event ) e2.copy();
2293 if ( !e2c.isEqual( e2 ) ) {
2296 Event e3 = new Event( 1, 2, 3 );
2297 if ( e3.isDuplication() ) {
2300 if ( e3.isSpeciation() ) {
2303 if ( e3.isGeneLoss() ) {
2306 if ( !e3.asText().toString().equals( "duplications [1] speciations [2] gene-losses [3]" ) ) {
2309 final Event e3c = ( Event ) e3.copy();
2310 final Event e3cc = ( Event ) e3c.copy();
2311 if ( !e3c.asSimpleText().toString().equals( "D2S3L" ) ) {
2315 if ( !e3c.isEqual( e3cc ) ) {
2318 Event e4 = new Event( 1, 2, 3 );
2319 if ( !e4.asText().toString().equals( "duplications [1] speciations [2] gene-losses [3]" ) ) {
2322 if ( !e4.asSimpleText().toString().equals( "D2S3L" ) ) {
2325 final Event e4c = ( Event ) e4.copy();
2327 final Event e4cc = ( Event ) e4c.copy();
2328 if ( !e4cc.asText().toString().equals( "duplications [1] speciations [2] gene-losses [3]" ) ) {
2331 if ( !e4c.isEqual( e4cc ) ) {
2334 final Event e5 = new Event();
2335 if ( !e5.isUnassigned() ) {
2338 if ( !e5.asText().toString().equals( "unassigned" ) ) {
2341 if ( !e5.asSimpleText().toString().equals( "" ) ) {
2344 final Event e6 = new Event( 1, 0, 0 );
2345 if ( !e6.asText().toString().equals( "duplication" ) ) {
2348 if ( !e6.asSimpleText().toString().equals( "D" ) ) {
2351 final Event e7 = new Event( 0, 1, 0 );
2352 if ( !e7.asText().toString().equals( "speciation" ) ) {
2355 if ( !e7.asSimpleText().toString().equals( "S" ) ) {
2358 final Event e8 = new Event( 0, 0, 1 );
2359 if ( !e8.asText().toString().equals( "gene-loss" ) ) {
2362 if ( !e8.asSimpleText().toString().equals( "L" ) ) {
2366 catch ( final Exception e ) {
2367 e.printStackTrace( System.out );
2373 private static boolean testDeletionOfExternalNodes() {
2375 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
2376 final Phylogeny t0 = factory.create( "A", new NHXParser() )[ 0 ];
2377 final PhylogenyWriter w = new PhylogenyWriter();
2378 if ( t0.isEmpty() ) {
2381 if ( t0.getNumberOfExternalNodes() != 1 ) {
2384 t0.deleteSubtree( t0.getNode( "A" ), false );
2385 if ( t0.getNumberOfExternalNodes() != 0 ) {
2388 if ( !t0.isEmpty() ) {
2391 final Phylogeny t1 = factory.create( "(A,B)r", new NHXParser() )[ 0 ];
2392 if ( t1.getNumberOfExternalNodes() != 2 ) {
2395 t1.deleteSubtree( t1.getNode( "A" ), false );
2396 if ( t1.getNumberOfExternalNodes() != 1 ) {
2399 if ( !t1.getNode( "B" ).getName().equals( "B" ) ) {
2402 t1.deleteSubtree( t1.getNode( "B" ), false );
2403 if ( t1.getNumberOfExternalNodes() != 1 ) {
2406 t1.deleteSubtree( t1.getNode( "r" ), false );
2407 if ( !t1.isEmpty() ) {
2410 final Phylogeny t2 = factory.create( "((A,B),C)", new NHXParser() )[ 0 ];
2411 if ( t2.getNumberOfExternalNodes() != 3 ) {
2414 t2.deleteSubtree( t2.getNode( "B" ), false );
2415 if ( t2.getNumberOfExternalNodes() != 2 ) {
2418 t2.toNewHampshireX();
2419 PhylogenyNode n = t2.getNode( "A" );
2420 if ( !n.getNextExternalNode().getName().equals( "C" ) ) {
2423 t2.deleteSubtree( t2.getNode( "A" ), false );
2424 if ( t2.getNumberOfExternalNodes() != 2 ) {
2427 t2.deleteSubtree( t2.getNode( "C" ), true );
2428 if ( t2.getNumberOfExternalNodes() != 1 ) {
2431 final Phylogeny t3 = factory.create( "((A,B),(C,D))", new NHXParser() )[ 0 ];
2432 if ( t3.getNumberOfExternalNodes() != 4 ) {
2435 t3.deleteSubtree( t3.getNode( "B" ), true );
2436 if ( t3.getNumberOfExternalNodes() != 3 ) {
2439 n = t3.getNode( "A" );
2440 if ( !n.getNextExternalNode().getName().equals( "C" ) ) {
2443 n = n.getNextExternalNode();
2444 if ( !n.getNextExternalNode().getName().equals( "D" ) ) {
2447 t3.deleteSubtree( t3.getNode( "A" ), true );
2448 if ( t3.getNumberOfExternalNodes() != 2 ) {
2451 n = t3.getNode( "C" );
2452 if ( !n.getNextExternalNode().getName().equals( "D" ) ) {
2455 t3.deleteSubtree( t3.getNode( "C" ), true );
2456 if ( t3.getNumberOfExternalNodes() != 1 ) {
2459 t3.deleteSubtree( t3.getNode( "D" ), true );
2460 if ( t3.getNumberOfExternalNodes() != 0 ) {
2463 final Phylogeny t4 = factory.create( "((A,((B11,B12),B2)),(C,D))", new NHXParser() )[ 0 ];
2464 if ( t4.getNumberOfExternalNodes() != 6 ) {
2467 t4.deleteSubtree( t4.getNode( "B2" ), true );
2468 if ( t4.getNumberOfExternalNodes() != 5 ) {
2471 String s = w.toNewHampshire( t4, false, true ).toString();
2472 if ( !s.equals( "((A,(B11,B12)),(C,D));" ) ) {
2475 t4.deleteSubtree( t4.getNode( "B11" ), true );
2476 if ( t4.getNumberOfExternalNodes() != 4 ) {
2479 t4.deleteSubtree( t4.getNode( "C" ), true );
2480 if ( t4.getNumberOfExternalNodes() != 3 ) {
2483 n = t4.getNode( "A" );
2484 n = n.getNextExternalNode();
2485 if ( !n.getName().equals( "B12" ) ) {
2488 n = n.getNextExternalNode();
2489 if ( !n.getName().equals( "D" ) ) {
2492 s = w.toNewHampshire( t4, false, true ).toString();
2493 if ( !s.equals( "((A,B12),D);" ) ) {
2496 final Phylogeny t5 = factory.create( "((A,((B11,B12),B2)),(C,D))", new NHXParser() )[ 0 ];
2497 t5.deleteSubtree( t5.getNode( "A" ), true );
2498 if ( t5.getNumberOfExternalNodes() != 5 ) {
2501 s = w.toNewHampshire( t5, false, true ).toString();
2502 if ( !s.equals( "(((B11,B12),B2),(C,D));" ) ) {
2505 final Phylogeny t6 = factory.create( "((A,((B11,B12),B2)),(C,D))", new NHXParser() )[ 0 ];
2506 t6.deleteSubtree( t6.getNode( "B11" ), true );
2507 if ( t6.getNumberOfExternalNodes() != 5 ) {
2510 s = w.toNewHampshire( t6, false, false ).toString();
2511 if ( !s.equals( "((A,(B12,B2)),(C,D));" ) ) {
2514 final Phylogeny t7 = factory.create( "((A,((B11,B12),B2)),(C,D))", new NHXParser() )[ 0 ];
2515 t7.deleteSubtree( t7.getNode( "B12" ), true );
2516 if ( t7.getNumberOfExternalNodes() != 5 ) {
2519 s = w.toNewHampshire( t7, false, true ).toString();
2520 if ( !s.equals( "((A,(B11,B2)),(C,D));" ) ) {
2523 final Phylogeny t8 = factory.create( "((A,((B11,B12),B2)),(C,D))", new NHXParser() )[ 0 ];
2524 t8.deleteSubtree( t8.getNode( "B2" ), true );
2525 if ( t8.getNumberOfExternalNodes() != 5 ) {
2528 s = w.toNewHampshire( t8, false, false ).toString();
2529 if ( !s.equals( "((A,(B11,B12)),(C,D));" ) ) {
2532 final Phylogeny t9 = factory.create( "((A,((B11,B12),B2)),(C,D))", new NHXParser() )[ 0 ];
2533 t9.deleteSubtree( t9.getNode( "C" ), true );
2534 if ( t9.getNumberOfExternalNodes() != 5 ) {
2537 s = w.toNewHampshire( t9, false, true ).toString();
2538 if ( !s.equals( "((A,((B11,B12),B2)),D);" ) ) {
2541 final Phylogeny t10 = factory.create( "((A,((B11,B12),B2)),(C,D))", new NHXParser() )[ 0 ];
2542 t10.deleteSubtree( t10.getNode( "D" ), true );
2543 if ( t10.getNumberOfExternalNodes() != 5 ) {
2546 s = w.toNewHampshire( t10, false, true ).toString();
2547 if ( !s.equals( "((A,((B11,B12),B2)),C);" ) ) {
2550 final Phylogeny t11 = factory.create( "(A,B,C)", new NHXParser() )[ 0 ];
2551 t11.deleteSubtree( t11.getNode( "A" ), true );
2552 if ( t11.getNumberOfExternalNodes() != 2 ) {
2555 s = w.toNewHampshire( t11, false, true ).toString();
2556 if ( !s.equals( "(B,C);" ) ) {
2559 t11.deleteSubtree( t11.getNode( "C" ), true );
2560 if ( t11.getNumberOfExternalNodes() != 1 ) {
2563 s = w.toNewHampshire( t11, false, false ).toString();
2564 if ( !s.equals( "B;" ) ) {
2567 final Phylogeny t12 = factory.create( "((A1,A2,A3),(B1,B2,B3),(C1,C2,C3))", new NHXParser() )[ 0 ];
2568 t12.deleteSubtree( t12.getNode( "B2" ), true );
2569 if ( t12.getNumberOfExternalNodes() != 8 ) {
2572 s = w.toNewHampshire( t12, false, true ).toString();
2573 if ( !s.equals( "((A1,A2,A3),(B1,B3),(C1,C2,C3));" ) ) {
2576 t12.deleteSubtree( t12.getNode( "B3" ), true );
2577 if ( t12.getNumberOfExternalNodes() != 7 ) {
2580 s = w.toNewHampshire( t12, false, true ).toString();
2581 if ( !s.equals( "((A1,A2,A3),B1,(C1,C2,C3));" ) ) {
2584 t12.deleteSubtree( t12.getNode( "C3" ), true );
2585 if ( t12.getNumberOfExternalNodes() != 6 ) {
2588 s = w.toNewHampshire( t12, false, true ).toString();
2589 if ( !s.equals( "((A1,A2,A3),B1,(C1,C2));" ) ) {
2592 t12.deleteSubtree( t12.getNode( "A1" ), true );
2593 if ( t12.getNumberOfExternalNodes() != 5 ) {
2596 s = w.toNewHampshire( t12, false, true ).toString();
2597 if ( !s.equals( "((A2,A3),B1,(C1,C2));" ) ) {
2600 t12.deleteSubtree( t12.getNode( "B1" ), true );
2601 if ( t12.getNumberOfExternalNodes() != 4 ) {
2604 s = w.toNewHampshire( t12, false, true ).toString();
2605 if ( !s.equals( "((A2,A3),(C1,C2));" ) ) {
2608 t12.deleteSubtree( t12.getNode( "A3" ), true );
2609 if ( t12.getNumberOfExternalNodes() != 3 ) {
2612 s = w.toNewHampshire( t12, false, true ).toString();
2613 if ( !s.equals( "(A2,(C1,C2));" ) ) {
2616 t12.deleteSubtree( t12.getNode( "A2" ), true );
2617 if ( t12.getNumberOfExternalNodes() != 2 ) {
2620 s = w.toNewHampshire( t12, false, true ).toString();
2621 if ( !s.equals( "(C1,C2);" ) ) {
2624 final Phylogeny t13 = factory.create( "(A,B,C,(D:1.0,E:2.0):3.0)", new NHXParser() )[ 0 ];
2625 t13.deleteSubtree( t13.getNode( "D" ), true );
2626 if ( t13.getNumberOfExternalNodes() != 4 ) {
2629 s = w.toNewHampshire( t13, false, true ).toString();
2630 if ( !s.equals( "(A,B,C,E:5.0);" ) ) {
2633 final Phylogeny t14 = factory.create( "((A,B,C,(D:0.1,E:0.4):1.0),F)", new NHXParser() )[ 0 ];
2634 t14.deleteSubtree( t14.getNode( "E" ), true );
2635 if ( t14.getNumberOfExternalNodes() != 5 ) {
2638 s = w.toNewHampshire( t14, false, true ).toString();
2639 if ( !s.equals( "((A,B,C,D:1.1),F);" ) ) {
2642 final Phylogeny t15 = factory.create( "((A1,A2,A3,A4),(B1,B2,B3,B4),(C1,C2,C3,C4))", new NHXParser() )[ 0 ];
2643 t15.deleteSubtree( t15.getNode( "B2" ), true );
2644 if ( t15.getNumberOfExternalNodes() != 11 ) {
2647 t15.deleteSubtree( t15.getNode( "B1" ), true );
2648 if ( t15.getNumberOfExternalNodes() != 10 ) {
2651 t15.deleteSubtree( t15.getNode( "B3" ), true );
2652 if ( t15.getNumberOfExternalNodes() != 9 ) {
2655 t15.deleteSubtree( t15.getNode( "B4" ), true );
2656 if ( t15.getNumberOfExternalNodes() != 8 ) {
2659 t15.deleteSubtree( t15.getNode( "A1" ), true );
2660 if ( t15.getNumberOfExternalNodes() != 7 ) {
2663 t15.deleteSubtree( t15.getNode( "C4" ), true );
2664 if ( t15.getNumberOfExternalNodes() != 6 ) {
2668 catch ( final Exception e ) {
2669 e.printStackTrace( System.out );
2675 private static boolean testDescriptiveStatistics() {
2677 final DescriptiveStatistics dss1 = new BasicDescriptiveStatistics();
2678 dss1.addValue( 82 );
2679 dss1.addValue( 78 );
2680 dss1.addValue( 70 );
2681 dss1.addValue( 58 );
2682 dss1.addValue( 42 );
2683 if ( dss1.getN() != 5 ) {
2686 if ( !Test.isEqual( dss1.getMin(), 42 ) ) {
2689 if ( !Test.isEqual( dss1.getMax(), 82 ) ) {
2692 if ( !Test.isEqual( dss1.arithmeticMean(), 66 ) ) {
2695 if ( !Test.isEqual( dss1.sampleStandardDeviation(), 16.24807680927192 ) ) {
2698 if ( !Test.isEqual( dss1.median(), 70 ) ) {
2701 if ( !Test.isEqual( dss1.midrange(), 62 ) ) {
2704 if ( !Test.isEqual( dss1.sampleVariance(), 264 ) ) {
2707 if ( !Test.isEqual( dss1.pearsonianSkewness(), -0.7385489458759964 ) ) {
2710 if ( !Test.isEqual( dss1.coefficientOfVariation(), 0.24618298195866547 ) ) {
2713 if ( !Test.isEqual( dss1.sampleStandardUnit( 66 - 16.24807680927192 ), -1.0 ) ) {
2716 if ( !Test.isEqual( dss1.getValue( 1 ), 78 ) ) {
2719 dss1.addValue( 123 );
2720 if ( !Test.isEqual( dss1.arithmeticMean(), 75.5 ) ) {
2723 if ( !Test.isEqual( dss1.getMax(), 123 ) ) {
2726 if ( !Test.isEqual( dss1.standardErrorOfMean(), 11.200446419674531 ) ) {
2729 final DescriptiveStatistics dss2 = new BasicDescriptiveStatistics();
2730 dss2.addValue( -1.85 );
2731 dss2.addValue( 57.5 );
2732 dss2.addValue( 92.78 );
2733 dss2.addValue( 57.78 );
2734 if ( !Test.isEqual( dss2.median(), 57.64 ) ) {
2737 if ( !Test.isEqual( dss2.sampleStandardDeviation(), 39.266984753946495 ) ) {
2740 final double[] a = dss2.getDataAsDoubleArray();
2741 if ( !Test.isEqual( a[ 3 ], 57.78 ) ) {
2744 dss2.addValue( -100 );
2745 if ( !Test.isEqual( dss2.sampleStandardDeviation(), 75.829111296388 ) ) {
2748 if ( !Test.isEqual( dss2.sampleVariance(), 5750.05412 ) ) {
2751 final double[] ds = new double[ 14 ];
2766 final int[] bins = BasicDescriptiveStatistics.performBinning( ds, 0, 40, 4 );
2767 if ( bins.length != 4 ) {
2770 if ( bins[ 0 ] != 2 ) {
2773 if ( bins[ 1 ] != 3 ) {
2776 if ( bins[ 2 ] != 4 ) {
2779 if ( bins[ 3 ] != 5 ) {
2782 final double[] ds1 = new double[ 9 ];
2792 final int[] bins1 = BasicDescriptiveStatistics.performBinning( ds1, 0, 40, 4 );
2793 if ( bins1.length != 4 ) {
2796 if ( bins1[ 0 ] != 2 ) {
2799 if ( bins1[ 1 ] != 3 ) {
2802 if ( bins1[ 2 ] != 0 ) {
2805 if ( bins1[ 3 ] != 4 ) {
2808 final int[] bins1_1 = BasicDescriptiveStatistics.performBinning( ds1, 0, 40, 3 );
2809 if ( bins1_1.length != 3 ) {
2812 if ( bins1_1[ 0 ] != 3 ) {
2815 if ( bins1_1[ 1 ] != 2 ) {
2818 if ( bins1_1[ 2 ] != 4 ) {
2821 final int[] bins1_2 = BasicDescriptiveStatistics.performBinning( ds1, 1, 39, 3 );
2822 if ( bins1_2.length != 3 ) {
2825 if ( bins1_2[ 0 ] != 2 ) {
2828 if ( bins1_2[ 1 ] != 2 ) {
2831 if ( bins1_2[ 2 ] != 2 ) {
2834 final DescriptiveStatistics dss3 = new BasicDescriptiveStatistics();
2848 dss3.addValue( 10 );
2849 dss3.addValue( 10 );
2850 dss3.addValue( 10 );
2851 final AsciiHistogram histo = new AsciiHistogram( dss3 );
2852 histo.toStringBuffer( 10, '=', 40, 5 );
2853 histo.toStringBuffer( 3, 8, 10, '=', 40, 5 );
2855 catch ( final Exception e ) {
2856 e.printStackTrace( System.out );
2862 private static boolean testDir( final String file ) {
2864 final File f = new File( file );
2865 if ( !f.exists() ) {
2868 if ( !f.isDirectory() ) {
2871 if ( !f.canRead() ) {
2875 catch ( final Exception e ) {
2881 private static boolean testExternalNodeRelatedMethods() {
2883 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
2884 final Phylogeny t1 = factory.create( "((A,B),(C,D))", new NHXParser() )[ 0 ];
2885 PhylogenyNode n = t1.getNode( "A" );
2886 n = n.getNextExternalNode();
2887 if ( !n.getName().equals( "B" ) ) {
2890 n = n.getNextExternalNode();
2891 if ( !n.getName().equals( "C" ) ) {
2894 n = n.getNextExternalNode();
2895 if ( !n.getName().equals( "D" ) ) {
2898 n = t1.getNode( "B" );
2899 while ( !n.isLastExternalNode() ) {
2900 n = n.getNextExternalNode();
2902 final Phylogeny t2 = factory.create( "(((A,B),C),D)", new NHXParser() )[ 0 ];
2903 n = t2.getNode( "A" );
2904 n = n.getNextExternalNode();
2905 if ( !n.getName().equals( "B" ) ) {
2908 n = n.getNextExternalNode();
2909 if ( !n.getName().equals( "C" ) ) {
2912 n = n.getNextExternalNode();
2913 if ( !n.getName().equals( "D" ) ) {
2916 n = t2.getNode( "B" );
2917 while ( !n.isLastExternalNode() ) {
2918 n = n.getNextExternalNode();
2920 final Phylogeny t3 = factory.create( "(((A,B),(C,D)),((E,F),(G,H)))", new NHXParser() )[ 0 ];
2921 n = t3.getNode( "A" );
2922 n = n.getNextExternalNode();
2923 if ( !n.getName().equals( "B" ) ) {
2926 n = n.getNextExternalNode();
2927 if ( !n.getName().equals( "C" ) ) {
2930 n = n.getNextExternalNode();
2931 if ( !n.getName().equals( "D" ) ) {
2934 n = n.getNextExternalNode();
2935 if ( !n.getName().equals( "E" ) ) {
2938 n = n.getNextExternalNode();
2939 if ( !n.getName().equals( "F" ) ) {
2942 n = n.getNextExternalNode();
2943 if ( !n.getName().equals( "G" ) ) {
2946 n = n.getNextExternalNode();
2947 if ( !n.getName().equals( "H" ) ) {
2950 n = t3.getNode( "B" );
2951 while ( !n.isLastExternalNode() ) {
2952 n = n.getNextExternalNode();
2954 final Phylogeny t4 = factory.create( "((A,B),(C,D))", new NHXParser() )[ 0 ];
2955 for( final PhylogenyNodeIterator iter = t4.iteratorExternalForward(); iter.hasNext(); ) {
2956 final PhylogenyNode node = iter.next();
2958 final Phylogeny t5 = factory.create( "(((A,B),(C,D)),((E,F),(G,H)))", new NHXParser() )[ 0 ];
2959 for( final PhylogenyNodeIterator iter = t5.iteratorExternalForward(); iter.hasNext(); ) {
2960 final PhylogenyNode node = iter.next();
2963 catch ( final Exception e ) {
2964 e.printStackTrace( System.out );
2970 private static boolean testGeneralTable() {
2972 final GeneralTable<Integer, String> t0 = new GeneralTable<Integer, String>();
2973 t0.setValue( 3, 2, "23" );
2974 t0.setValue( 10, 1, "error" );
2975 t0.setValue( 10, 1, "110" );
2976 t0.setValue( 9, 1, "19" );
2977 t0.setValue( 1, 10, "101" );
2978 t0.setValue( 10, 10, "1010" );
2979 t0.setValue( 100, 10, "10100" );
2980 t0.setValue( 0, 0, "00" );
2981 if ( !t0.getValue( 3, 2 ).equals( "23" ) ) {
2984 if ( !t0.getValue( 10, 1 ).equals( "110" ) ) {
2987 if ( !t0.getValueAsString( 1, 10 ).equals( "101" ) ) {
2990 if ( !t0.getValueAsString( 10, 10 ).equals( "1010" ) ) {
2993 if ( !t0.getValueAsString( 100, 10 ).equals( "10100" ) ) {
2996 if ( !t0.getValueAsString( 9, 1 ).equals( "19" ) ) {
2999 if ( !t0.getValueAsString( 0, 0 ).equals( "00" ) ) {
3002 if ( !t0.getValueAsString( 49, 4 ).equals( "" ) ) {
3005 if ( !t0.getValueAsString( 22349, 3434344 ).equals( "" ) ) {
3008 final GeneralTable<String, String> t1 = new GeneralTable<String, String>();
3009 t1.setValue( "3", "2", "23" );
3010 t1.setValue( "10", "1", "error" );
3011 t1.setValue( "10", "1", "110" );
3012 t1.setValue( "9", "1", "19" );
3013 t1.setValue( "1", "10", "101" );
3014 t1.setValue( "10", "10", "1010" );
3015 t1.setValue( "100", "10", "10100" );
3016 t1.setValue( "0", "0", "00" );
3017 t1.setValue( "qwerty", "zxcvbnm", "asdef" );
3018 if ( !t1.getValue( "3", "2" ).equals( "23" ) ) {
3021 if ( !t1.getValue( "10", "1" ).equals( "110" ) ) {
3024 if ( !t1.getValueAsString( "1", "10" ).equals( "101" ) ) {
3027 if ( !t1.getValueAsString( "10", "10" ).equals( "1010" ) ) {
3030 if ( !t1.getValueAsString( "100", "10" ).equals( "10100" ) ) {
3033 if ( !t1.getValueAsString( "9", "1" ).equals( "19" ) ) {
3036 if ( !t1.getValueAsString( "0", "0" ).equals( "00" ) ) {
3039 if ( !t1.getValueAsString( "qwerty", "zxcvbnm" ).equals( "asdef" ) ) {
3042 if ( !t1.getValueAsString( "49", "4" ).equals( "" ) ) {
3045 if ( !t1.getValueAsString( "22349", "3434344" ).equals( "" ) ) {
3049 catch ( final Exception e ) {
3050 e.printStackTrace( System.out );
3056 private static boolean testGetDistance() {
3058 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
3059 final Phylogeny p1 = factory.create( "(((A:1,B:2,X:100)ab:3,C:4)abc:5,(D:7,(E:9,F:10)ef:8)def:6)r",
3060 new NHXParser() )[ 0 ];
3061 final PhylogenyMethods pm = PhylogenyMethods.getInstance();
3062 if ( pm.calculateDistance( p1.getNode( "C" ), p1.getNode( "C" ) ) != 0 ) {
3065 if ( pm.calculateDistance( p1.getNode( "def" ), p1.getNode( "def" ) ) != 0 ) {
3068 if ( pm.calculateDistance( p1.getNode( "ef" ), p1.getNode( "ef" ) ) != 0 ) {
3071 if ( pm.calculateDistance( p1.getNode( "r" ), p1.getNode( "r" ) ) != 0 ) {
3074 if ( pm.calculateDistance( p1.getNode( "A" ), p1.getNode( "A" ) ) != 0 ) {
3077 if ( pm.calculateDistance( p1.getNode( "A" ), p1.getNode( "B" ) ) != 3 ) {
3080 if ( pm.calculateDistance( p1.getNode( "B" ), p1.getNode( "A" ) ) != 3 ) {
3083 if ( pm.calculateDistance( p1.getNode( "A" ), p1.getNode( "C" ) ) != 8 ) {
3086 if ( pm.calculateDistance( p1.getNode( "C" ), p1.getNode( "A" ) ) != 8 ) {
3089 if ( pm.calculateDistance( p1.getNode( "A" ), p1.getNode( "D" ) ) != 22 ) {
3092 if ( pm.calculateDistance( p1.getNode( "A" ), p1.getNode( "E" ) ) != 32 ) {
3095 if ( pm.calculateDistance( p1.getNode( "E" ), p1.getNode( "A" ) ) != 32 ) {
3098 if ( pm.calculateDistance( p1.getNode( "A" ), p1.getNode( "F" ) ) != 33 ) {
3101 if ( pm.calculateDistance( p1.getNode( "F" ), p1.getNode( "A" ) ) != 33 ) {
3104 if ( pm.calculateDistance( p1.getNode( "A" ), p1.getNode( "ab" ) ) != 1 ) {
3107 if ( pm.calculateDistance( p1.getNode( "ab" ), p1.getNode( "A" ) ) != 1 ) {
3110 if ( pm.calculateDistance( p1.getNode( "A" ), p1.getNode( "abc" ) ) != 4 ) {
3113 if ( pm.calculateDistance( p1.getNode( "abc" ), p1.getNode( "A" ) ) != 4 ) {
3116 if ( pm.calculateDistance( p1.getNode( "A" ), p1.getNode( "r" ) ) != 9 ) {
3119 if ( pm.calculateDistance( p1.getNode( "r" ), p1.getNode( "A" ) ) != 9 ) {
3122 if ( pm.calculateDistance( p1.getNode( "A" ), p1.getNode( "def" ) ) != 15 ) {
3125 if ( pm.calculateDistance( p1.getNode( "def" ), p1.getNode( "A" ) ) != 15 ) {
3128 if ( pm.calculateDistance( p1.getNode( "A" ), p1.getNode( "ef" ) ) != 23 ) {
3131 if ( pm.calculateDistance( p1.getNode( "ef" ), p1.getNode( "A" ) ) != 23 ) {
3134 if ( pm.calculateDistance( p1.getNode( "ef" ), p1.getNode( "def" ) ) != 8 ) {
3137 if ( pm.calculateDistance( p1.getNode( "def" ), p1.getNode( "ef" ) ) != 8 ) {
3140 if ( pm.calculateDistance( p1.getNode( "ef" ), p1.getNode( "r" ) ) != 14 ) {
3143 if ( pm.calculateDistance( p1.getNode( "ef" ), p1.getNode( "abc" ) ) != 19 ) {
3146 if ( pm.calculateDistance( p1.getNode( "ef" ), p1.getNode( "ab" ) ) != 22 ) {
3149 if ( pm.calculateDistance( p1.getNode( "ab" ), p1.getNode( "ef" ) ) != 22 ) {
3152 if ( pm.calculateDistance( p1.getNode( "def" ), p1.getNode( "abc" ) ) != 11 ) {
3155 final Phylogeny p2 = factory.create( "((A:4,B:5,C:6)abc:1,(D:7,E:8,F:9)def:2,(G:10,H:11,I:12)ghi:3)r",
3156 new NHXParser() )[ 0 ];
3157 if ( pm.calculateDistance( p2.getNode( "A" ), p2.getNode( "B" ) ) != 9 ) {
3160 if ( pm.calculateDistance( p2.getNode( "A" ), p2.getNode( "C" ) ) != 10 ) {
3163 if ( pm.calculateDistance( p2.getNode( "A" ), p2.getNode( "D" ) ) != 14 ) {
3166 if ( pm.calculateDistance( p2.getNode( "A" ), p2.getNode( "ghi" ) ) != 8 ) {
3169 if ( pm.calculateDistance( p2.getNode( "A" ), p2.getNode( "I" ) ) != 20 ) {
3172 if ( pm.calculateDistance( p2.getNode( "G" ), p2.getNode( "ghi" ) ) != 10 ) {
3175 if ( pm.calculateDistance( p2.getNode( "r" ), p2.getNode( "r" ) ) != 0 ) {
3178 if ( pm.calculateDistance( p2.getNode( "r" ), p2.getNode( "G" ) ) != 13 ) {
3181 if ( pm.calculateDistance( p2.getNode( "G" ), p2.getNode( "r" ) ) != 13 ) {
3184 if ( pm.calculateDistance( p2.getNode( "G" ), p2.getNode( "H" ) ) != 21 ) {
3187 if ( pm.calculateDistance( p2.getNode( "G" ), p2.getNode( "I" ) ) != 22 ) {
3191 catch ( final Exception e ) {
3192 e.printStackTrace( System.out );
3198 private static boolean testGetLCA() {
3200 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
3201 final Phylogeny p1 = factory.create( "((((((A,B)ab,C)abc,D)abcd,E)abcde,F)abcdef,(G,H)gh)abcdefgh",
3202 new NHXParser() )[ 0 ];
3203 final PhylogenyMethods pm = PhylogenyMethods.getInstance();
3204 final PhylogenyNode A = pm.obtainLCA( p1.getNode( "A" ), p1.getNode( "A" ) );
3205 if ( !A.getName().equals( "A" ) ) {
3208 final PhylogenyNode gh = pm.obtainLCA( p1.getNode( "gh" ), p1.getNode( "gh" ) );
3209 if ( !gh.getName().equals( "gh" ) ) {
3212 final PhylogenyNode ab = pm.obtainLCA( p1.getNode( "A" ), p1.getNode( "B" ) );
3213 if ( !ab.getName().equals( "ab" ) ) {
3216 final PhylogenyNode ab2 = pm.obtainLCA( p1.getNode( "B" ), p1.getNode( "A" ) );
3217 if ( !ab2.getName().equals( "ab" ) ) {
3220 final PhylogenyNode gh2 = pm.obtainLCA( p1.getNode( "H" ), p1.getNode( "G" ) );
3221 if ( !gh2.getName().equals( "gh" ) ) {
3224 final PhylogenyNode gh3 = pm.obtainLCA( p1.getNode( "G" ), p1.getNode( "H" ) );
3225 if ( !gh3.getName().equals( "gh" ) ) {
3228 final PhylogenyNode abc = pm.obtainLCA( p1.getNode( "C" ), p1.getNode( "A" ) );
3229 if ( !abc.getName().equals( "abc" ) ) {
3232 final PhylogenyNode abc2 = pm.obtainLCA( p1.getNode( "A" ), p1.getNode( "C" ) );
3233 if ( !abc2.getName().equals( "abc" ) ) {
3236 final PhylogenyNode abcd = pm.obtainLCA( p1.getNode( "A" ), p1.getNode( "D" ) );
3237 if ( !abcd.getName().equals( "abcd" ) ) {
3240 final PhylogenyNode abcd2 = pm.obtainLCA( p1.getNode( "D" ), p1.getNode( "A" ) );
3241 if ( !abcd2.getName().equals( "abcd" ) ) {
3244 final PhylogenyNode abcdef = pm.obtainLCA( p1.getNode( "A" ), p1.getNode( "F" ) );
3245 if ( !abcdef.getName().equals( "abcdef" ) ) {
3248 final PhylogenyNode abcdef2 = pm.obtainLCA( p1.getNode( "F" ), p1.getNode( "A" ) );
3249 if ( !abcdef2.getName().equals( "abcdef" ) ) {
3252 final PhylogenyNode abcdef3 = pm.obtainLCA( p1.getNode( "ab" ), p1.getNode( "F" ) );
3253 if ( !abcdef3.getName().equals( "abcdef" ) ) {
3256 final PhylogenyNode abcdef4 = pm.obtainLCA( p1.getNode( "F" ), p1.getNode( "ab" ) );
3257 if ( !abcdef4.getName().equals( "abcdef" ) ) {
3260 final PhylogenyNode abcde = pm.obtainLCA( p1.getNode( "A" ), p1.getNode( "E" ) );
3261 if ( !abcde.getName().equals( "abcde" ) ) {
3264 final PhylogenyNode abcde2 = pm.obtainLCA( p1.getNode( "E" ), p1.getNode( "A" ) );
3265 if ( !abcde2.getName().equals( "abcde" ) ) {
3268 final PhylogenyNode r = pm.obtainLCA( p1.getNode( "abcdefgh" ), p1.getNode( "abcdefgh" ) );
3269 if ( !r.getName().equals( "abcdefgh" ) ) {
3272 final PhylogenyNode r2 = pm.obtainLCA( p1.getNode( "A" ), p1.getNode( "H" ) );
3273 if ( !r2.getName().equals( "abcdefgh" ) ) {
3276 final PhylogenyNode r3 = pm.obtainLCA( p1.getNode( "H" ), p1.getNode( "A" ) );
3277 if ( !r3.getName().equals( "abcdefgh" ) ) {
3280 final PhylogenyNode abcde3 = pm.obtainLCA( p1.getNode( "E" ), p1.getNode( "abcde" ) );
3281 if ( !abcde3.getName().equals( "abcde" ) ) {
3284 final PhylogenyNode abcde4 = pm.obtainLCA( p1.getNode( "abcde" ), p1.getNode( "E" ) );
3285 if ( !abcde4.getName().equals( "abcde" ) ) {
3288 final PhylogenyNode ab3 = pm.obtainLCA( p1.getNode( "ab" ), p1.getNode( "B" ) );
3289 if ( !ab3.getName().equals( "ab" ) ) {
3292 final PhylogenyNode ab4 = pm.obtainLCA( p1.getNode( "B" ), p1.getNode( "ab" ) );
3293 if ( !ab4.getName().equals( "ab" ) ) {
3296 final Phylogeny p2 = factory.create( "(a,b,(((c,d)cd,e)cde,f)cdef)r", new NHXParser() )[ 0 ];
3297 final PhylogenyNode cd = pm.obtainLCA( p2.getNode( "c" ), p2.getNode( "d" ) );
3298 if ( !cd.getName().equals( "cd" ) ) {
3301 final PhylogenyNode cd2 = pm.obtainLCA( p2.getNode( "d" ), p2.getNode( "c" ) );
3302 if ( !cd2.getName().equals( "cd" ) ) {
3305 final PhylogenyNode cde = pm.obtainLCA( p2.getNode( "c" ), p2.getNode( "e" ) );
3306 if ( !cde.getName().equals( "cde" ) ) {
3309 final PhylogenyNode cde2 = pm.obtainLCA( p2.getNode( "e" ), p2.getNode( "c" ) );
3310 if ( !cde2.getName().equals( "cde" ) ) {
3313 final PhylogenyNode cdef = pm.obtainLCA( p2.getNode( "c" ), p2.getNode( "f" ) );
3314 if ( !cdef.getName().equals( "cdef" ) ) {
3317 final PhylogenyNode cdef2 = pm.obtainLCA( p2.getNode( "d" ), p2.getNode( "f" ) );
3318 if ( !cdef2.getName().equals( "cdef" ) ) {
3321 final PhylogenyNode cdef3 = pm.obtainLCA( p2.getNode( "f" ), p2.getNode( "d" ) );
3322 if ( !cdef3.getName().equals( "cdef" ) ) {
3325 final PhylogenyNode rt = pm.obtainLCA( p2.getNode( "c" ), p2.getNode( "a" ) );
3326 if ( !rt.getName().equals( "r" ) ) {
3329 final Phylogeny p3 = factory
3330 .create( "((((a,(b,c)bc)abc,(d,e)de)abcde,f)abcdef,(((g,h)gh,(i,j)ij)ghij,k)ghijk,l)",
3331 new NHXParser() )[ 0 ];
3332 final PhylogenyNode bc_3 = pm.obtainLCA( p3.getNode( "b" ), p3.getNode( "c" ) );
3333 if ( !bc_3.getName().equals( "bc" ) ) {
3336 final PhylogenyNode ac_3 = pm.obtainLCA( p3.getNode( "a" ), p3.getNode( "c" ) );
3337 if ( !ac_3.getName().equals( "abc" ) ) {
3340 final PhylogenyNode ad_3 = pm.obtainLCA( p3.getNode( "a" ), p3.getNode( "d" ) );
3341 if ( !ad_3.getName().equals( "abcde" ) ) {
3344 final PhylogenyNode af_3 = pm.obtainLCA( p3.getNode( "a" ), p3.getNode( "f" ) );
3345 if ( !af_3.getName().equals( "abcdef" ) ) {
3348 final PhylogenyNode ag_3 = pm.obtainLCA( p3.getNode( "a" ), p3.getNode( "g" ) );
3349 if ( !ag_3.getName().equals( "" ) ) {
3352 if ( !ag_3.isRoot() ) {
3355 final PhylogenyNode al_3 = pm.obtainLCA( p3.getNode( "a" ), p3.getNode( "l" ) );
3356 if ( !al_3.getName().equals( "" ) ) {
3359 if ( !al_3.isRoot() ) {
3362 final PhylogenyNode kl_3 = pm.obtainLCA( p3.getNode( "k" ), p3.getNode( "l" ) );
3363 if ( !kl_3.getName().equals( "" ) ) {
3366 if ( !kl_3.isRoot() ) {
3369 final PhylogenyNode fl_3 = pm.obtainLCA( p3.getNode( "f" ), p3.getNode( "l" ) );
3370 if ( !fl_3.getName().equals( "" ) ) {
3373 if ( !fl_3.isRoot() ) {
3376 final PhylogenyNode gk_3 = pm.obtainLCA( p3.getNode( "g" ), p3.getNode( "k" ) );
3377 if ( !gk_3.getName().equals( "ghijk" ) ) {
3380 final Phylogeny p4 = factory.create( "(a,b,c)r", new NHXParser() )[ 0 ];
3381 final PhylogenyNode r_4 = pm.obtainLCA( p4.getNode( "b" ), p4.getNode( "c" ) );
3382 if ( !r_4.getName().equals( "r" ) ) {
3385 final Phylogeny p5 = factory.create( "((a,b),c,d)root", new NHXParser() )[ 0 ];
3386 final PhylogenyNode r_5 = pm.obtainLCA( p5.getNode( "a" ), p5.getNode( "c" ) );
3387 if ( !r_5.getName().equals( "root" ) ) {
3390 final Phylogeny p6 = factory.create( "((a,b),c,d)rot", new NHXParser() )[ 0 ];
3391 final PhylogenyNode r_6 = pm.obtainLCA( p6.getNode( "c" ), p6.getNode( "a" ) );
3392 if ( !r_6.getName().equals( "rot" ) ) {
3395 final Phylogeny p7 = factory.create( "(((a,b)x,c)x,d,e)rott", new NHXParser() )[ 0 ];
3396 final PhylogenyNode r_7 = pm.obtainLCA( p7.getNode( "a" ), p7.getNode( "e" ) );
3397 if ( !r_7.getName().equals( "rott" ) ) {
3401 catch ( final Exception e ) {
3402 e.printStackTrace( System.out );
3408 private static boolean testHmmscanOutputParser() {
3409 final String test_dir = Test.PATH_TO_TEST_DATA;
3411 final HmmscanPerDomainTableParser parser1 = new HmmscanPerDomainTableParser( new File( test_dir
3412 + ForesterUtil.getFileSeparator() + "hmmscan30b3_output_1" ), "MONBR", INDIVIDUAL_SCORE_CUTOFF.NONE );
3414 final HmmscanPerDomainTableParser parser2 = new HmmscanPerDomainTableParser( new File( test_dir
3415 + ForesterUtil.getFileSeparator() + "hmmscan30b3_output_2" ), "MONBR", INDIVIDUAL_SCORE_CUTOFF.NONE );
3416 final List<Protein> proteins = parser2.parse();
3417 if ( parser2.getProteinsEncountered() != 4 ) {
3420 if ( proteins.size() != 4 ) {
3423 if ( parser2.getDomainsEncountered() != 69 ) {
3426 if ( parser2.getDomainsIgnoredDueToDuf() != 0 ) {
3429 if ( parser2.getDomainsIgnoredDueToEval() != 0 ) {
3432 final Protein p1 = proteins.get( 0 );
3433 if ( p1.getNumberOfProteinDomains() != 15 ) {
3436 if ( p1.getLength() != 850 ) {
3439 final Protein p2 = proteins.get( 1 );
3440 if ( p2.getNumberOfProteinDomains() != 51 ) {
3443 if ( p2.getLength() != 1291 ) {
3446 final Protein p3 = proteins.get( 2 );
3447 if ( p3.getNumberOfProteinDomains() != 2 ) {
3450 final Protein p4 = proteins.get( 3 );
3451 if ( p4.getNumberOfProteinDomains() != 1 ) {
3454 if ( !p4.getProteinDomain( 0 ).getDomainId().toString().equals( "DNA_pol_B_new" ) ) {
3457 if ( p4.getProteinDomain( 0 ).getFrom() != 51 ) {
3460 if ( p4.getProteinDomain( 0 ).getTo() != 395 ) {
3463 if ( !Test.isEqual( p4.getProteinDomain( 0 ).getPerDomainEvalue(), 1.2e-39 ) ) {
3466 if ( !Test.isEqual( p4.getProteinDomain( 0 ).getPerDomainScore(), 135.7 ) ) {
3469 if ( !Test.isEqual( p4.getProteinDomain( 0 ).getPerSequenceEvalue(), 8.3e-40 ) ) {
3472 if ( !Test.isEqual( p4.getProteinDomain( 0 ).getPerSequenceScore(), 136.3 ) ) {
3475 if ( !Test.isEqual( p4.getProteinDomain( 0 ).getNumber(), 1 ) ) {
3478 if ( !Test.isEqual( p4.getProteinDomain( 0 ).getTotalCount(), 1 ) ) {
3482 catch ( final Exception e ) {
3483 e.printStackTrace( System.out );
3489 private static boolean testLastExternalNodeMethods() {
3491 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
3492 final char[] a0 = { '(', '(', 'A', ',', 'B', ')', ',', '(', 'C', ',', 'D', ')', ')', };
3493 final Phylogeny t0 = factory.create( a0, new NHXParser() )[ 0 ];
3494 final PhylogenyNode n1 = t0.getNode( "A" );
3495 if ( n1.isLastExternalNode() ) {
3498 final PhylogenyNode n2 = t0.getNode( "B" );
3499 if ( n2.isLastExternalNode() ) {
3502 final PhylogenyNode n3 = t0.getNode( "C" );
3503 if ( n3.isLastExternalNode() ) {
3506 final PhylogenyNode n4 = t0.getNode( "D" );
3507 if ( !n4.isLastExternalNode() ) {
3511 catch ( final Exception e ) {
3512 e.printStackTrace( System.out );
3518 private static boolean testLevelOrderIterator() {
3520 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
3521 final Phylogeny t0 = factory.create( "((A,B)ab,(C,D)cd)r", new NHXParser() )[ 0 ];
3522 PhylogenyNodeIterator it0;
3523 for( it0 = t0.iteratorLevelOrder(); it0.hasNext(); ) {
3526 for( it0.reset(); it0.hasNext(); ) {
3529 final PhylogenyNodeIterator it = t0.iteratorLevelOrder();
3530 if ( !it.next().getName().equals( "r" ) ) {
3533 if ( !it.next().getName().equals( "ab" ) ) {
3536 if ( !it.next().getName().equals( "cd" ) ) {
3539 if ( !it.next().getName().equals( "A" ) ) {
3542 if ( !it.next().getName().equals( "B" ) ) {
3545 if ( !it.next().getName().equals( "C" ) ) {
3548 if ( !it.next().getName().equals( "D" ) ) {
3551 if ( it.hasNext() ) {
3554 final Phylogeny t2 = factory.create( "(((1,2,(a,(X,Y,Z)b)3,4,5,6)A,B,C)abc,(D,E,(f1,(f21)f2,f3)F,G)defg)r",
3555 new NHXParser() )[ 0 ];
3556 PhylogenyNodeIterator it2;
3557 for( it2 = t2.iteratorLevelOrder(); it2.hasNext(); ) {
3560 for( it2.reset(); it2.hasNext(); ) {
3563 final PhylogenyNodeIterator it3 = t2.iteratorLevelOrder();
3564 if ( !it3.next().getName().equals( "r" ) ) {
3567 if ( !it3.next().getName().equals( "abc" ) ) {
3570 if ( !it3.next().getName().equals( "defg" ) ) {
3573 if ( !it3.next().getName().equals( "A" ) ) {
3576 if ( !it3.next().getName().equals( "B" ) ) {
3579 if ( !it3.next().getName().equals( "C" ) ) {
3582 if ( !it3.next().getName().equals( "D" ) ) {
3585 if ( !it3.next().getName().equals( "E" ) ) {
3588 if ( !it3.next().getName().equals( "F" ) ) {
3591 if ( !it3.next().getName().equals( "G" ) ) {
3594 if ( !it3.next().getName().equals( "1" ) ) {
3597 if ( !it3.next().getName().equals( "2" ) ) {
3600 if ( !it3.next().getName().equals( "3" ) ) {
3603 if ( !it3.next().getName().equals( "4" ) ) {
3606 if ( !it3.next().getName().equals( "5" ) ) {
3609 if ( !it3.next().getName().equals( "6" ) ) {
3612 if ( !it3.next().getName().equals( "f1" ) ) {
3615 if ( !it3.next().getName().equals( "f2" ) ) {
3618 if ( !it3.next().getName().equals( "f3" ) ) {
3621 if ( !it3.next().getName().equals( "a" ) ) {
3624 if ( !it3.next().getName().equals( "b" ) ) {
3627 if ( !it3.next().getName().equals( "f21" ) ) {
3630 if ( !it3.next().getName().equals( "X" ) ) {
3633 if ( !it3.next().getName().equals( "Y" ) ) {
3636 if ( !it3.next().getName().equals( "Z" ) ) {
3639 if ( it3.hasNext() ) {
3642 final Phylogeny t4 = factory.create( "((((D)C)B)A)r", new NHXParser() )[ 0 ];
3643 PhylogenyNodeIterator it4;
3644 for( it4 = t4.iteratorLevelOrder(); it4.hasNext(); ) {
3647 for( it4.reset(); it4.hasNext(); ) {
3650 final PhylogenyNodeIterator it5 = t4.iteratorLevelOrder();
3651 if ( !it5.next().getName().equals( "r" ) ) {
3654 if ( !it5.next().getName().equals( "A" ) ) {
3657 if ( !it5.next().getName().equals( "B" ) ) {
3660 if ( !it5.next().getName().equals( "C" ) ) {
3663 if ( !it5.next().getName().equals( "D" ) ) {
3666 final Phylogeny t5 = factory.create( "A", new NHXParser() )[ 0 ];
3667 PhylogenyNodeIterator it6;
3668 for( it6 = t5.iteratorLevelOrder(); it6.hasNext(); ) {
3671 for( it6.reset(); it6.hasNext(); ) {
3674 final PhylogenyNodeIterator it7 = t5.iteratorLevelOrder();
3675 if ( !it7.next().getName().equals( "A" ) ) {
3678 if ( it.hasNext() ) {
3682 catch ( final Exception e ) {
3683 e.printStackTrace( System.out );
3689 private static boolean testMidpointrooting() {
3691 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
3692 final Phylogeny t1 = factory.create( "((A:1,B:2)AB:1[&&NHX:B=55],(C:3,D:4)CD:3[&&NHX:B=10])ABCD:0.5",
3693 new NHXParser() )[ 0 ];
3694 if ( !t1.isRooted() ) {
3697 PhylogenyMethods.midpointRoot( t1 );
3698 if ( !isEqual( t1.getNode( "A" ).getDistanceToParent(), 1 ) ) {
3701 if ( !isEqual( t1.getNode( "B" ).getDistanceToParent(), 2 ) ) {
3704 if ( !isEqual( t1.getNode( "C" ).getDistanceToParent(), 3 ) ) {
3707 if ( !isEqual( t1.getNode( "D" ).getDistanceToParent(), 4 ) ) {
3710 if ( !isEqual( t1.getNode( "CD" ).getDistanceToParent(), 1 ) ) {
3713 if ( !isEqual( t1.getNode( "AB" ).getDistanceToParent(), 3 ) ) {
3716 t1.reRoot( t1.getNode( "A" ) );
3717 PhylogenyMethods.midpointRoot( t1 );
3718 if ( !isEqual( t1.getNode( "A" ).getDistanceToParent(), 1 ) ) {
3721 if ( !isEqual( t1.getNode( "B" ).getDistanceToParent(), 2 ) ) {
3724 if ( !isEqual( t1.getNode( "C" ).getDistanceToParent(), 3 ) ) {
3727 if ( !isEqual( t1.getNode( "D" ).getDistanceToParent(), 4 ) ) {
3730 if ( !isEqual( t1.getNode( "CD" ).getDistanceToParent(), 1 ) ) {
3733 if ( !isEqual( t1.getNode( "AB" ).getDistanceToParent(), 3 ) ) {
3737 catch ( final Exception e ) {
3738 e.printStackTrace( System.out );
3744 private static boolean testNexusCharactersParsing() {
3746 final NexusCharactersParser parser = new NexusCharactersParser();
3747 parser.setSource( new File( Test.PATH_TO_TEST_DATA + "nexus_test_7.nex" ) );
3749 String[] labels = parser.getCharStateLabels();
3750 if ( labels.length != 7 ) {
3753 if ( !labels[ 0 ].equals( "14-3-3" ) ) {
3756 if ( !labels[ 1 ].equals( "2-Hacid_dh" ) ) {
3759 if ( !labels[ 2 ].equals( "2-Hacid_dh_C" ) ) {
3762 if ( !labels[ 3 ].equals( "2-oxoacid_dh" ) ) {
3765 if ( !labels[ 4 ].equals( "2OG-FeII_Oxy" ) ) {
3768 if ( !labels[ 5 ].equals( "3-HAO" ) ) {
3771 if ( !labels[ 6 ].equals( "3_5_exonuc" ) ) {
3774 parser.setSource( new File( Test.PATH_TO_TEST_DATA + "nexus_test_8.nex" ) );
3776 labels = parser.getCharStateLabels();
3777 if ( labels.length != 7 ) {
3780 if ( !labels[ 0 ].equals( "14-3-3" ) ) {
3783 if ( !labels[ 1 ].equals( "2-Hacid_dh" ) ) {
3786 if ( !labels[ 2 ].equals( "2-Hacid_dh_C" ) ) {
3789 if ( !labels[ 3 ].equals( "2-oxoacid_dh" ) ) {
3792 if ( !labels[ 4 ].equals( "2OG-FeII_Oxy" ) ) {
3795 if ( !labels[ 5 ].equals( "3-HAO" ) ) {
3798 if ( !labels[ 6 ].equals( "3_5_exonuc" ) ) {
3802 catch ( final Exception e ) {
3803 e.printStackTrace( System.out );
3809 private static boolean testNexusMatrixParsing() {
3811 final NexusBinaryStatesMatrixParser parser = new NexusBinaryStatesMatrixParser();
3812 parser.setSource( new File( Test.PATH_TO_TEST_DATA + "nexus_test_9.nex" ) );
3814 final CharacterStateMatrix<BinaryStates> m = parser.getMatrix();
3815 if ( m.getNumberOfCharacters() != 9 ) {
3818 if ( m.getNumberOfIdentifiers() != 5 ) {
3821 if ( m.getState( 0, 0 ) != BinaryStates.PRESENT ) {
3824 if ( m.getState( 0, 1 ) != BinaryStates.ABSENT ) {
3827 if ( m.getState( 1, 0 ) != BinaryStates.PRESENT ) {
3830 if ( m.getState( 2, 0 ) != BinaryStates.ABSENT ) {
3833 if ( m.getState( 4, 8 ) != BinaryStates.PRESENT ) {
3836 if ( !m.getIdentifier( 0 ).equals( "MOUSE" ) ) {
3839 if ( !m.getIdentifier( 4 ).equals( "ARATH" ) ) {
3842 // if ( labels.length != 7 ) {
3845 // if ( !labels[ 0 ].equals( "14-3-3" ) ) {
3848 // if ( !labels[ 1 ].equals( "2-Hacid_dh" ) ) {
3851 // if ( !labels[ 2 ].equals( "2-Hacid_dh_C" ) ) {
3854 // if ( !labels[ 3 ].equals( "2-oxoacid_dh" ) ) {
3857 // if ( !labels[ 4 ].equals( "2OG-FeII_Oxy" ) ) {
3860 // if ( !labels[ 5 ].equals( "3-HAO" ) ) {
3863 // if ( !labels[ 6 ].equals( "3_5_exonuc" ) ) {
3866 // parser.setSource( new File( Test.PATH_TO_TEST_DATA + "nexus_test_8.nex" ) );
3868 // labels = parser.getCharStateLabels();
3869 // if ( labels.length != 7 ) {
3872 // if ( !labels[ 0 ].equals( "14-3-3" ) ) {
3875 // if ( !labels[ 1 ].equals( "2-Hacid_dh" ) ) {
3878 // if ( !labels[ 2 ].equals( "2-Hacid_dh_C" ) ) {
3881 // if ( !labels[ 3 ].equals( "2-oxoacid_dh" ) ) {
3884 // if ( !labels[ 4 ].equals( "2OG-FeII_Oxy" ) ) {
3887 // if ( !labels[ 5 ].equals( "3-HAO" ) ) {
3890 // if ( !labels[ 6 ].equals( "3_5_exonuc" ) ) {
3894 catch ( final Exception e ) {
3895 e.printStackTrace( System.out );
3901 private static boolean testNexusTreeParsing() {
3903 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
3904 final NexusPhylogeniesParser parser = new NexusPhylogeniesParser();
3905 Phylogeny[] phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_1.nex", parser );
3906 if ( phylogenies.length != 1 ) {
3909 if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 25 ) {
3912 if ( !phylogenies[ 0 ].getName().equals( "" ) ) {
3916 phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_2.nex", parser );
3917 if ( phylogenies.length != 1 ) {
3920 if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 10 ) {
3923 if ( !phylogenies[ 0 ].getName().equals( "name" ) ) {
3927 phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_3.nex", parser );
3928 if ( phylogenies.length != 1 ) {
3931 if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 3 ) {
3934 if ( !phylogenies[ 0 ].getName().equals( "" ) ) {
3937 if ( phylogenies[ 0 ].isRooted() ) {
3941 phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_4.nex", parser );
3942 if ( phylogenies.length != 18 ) {
3945 if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 10 ) {
3948 if ( !phylogenies[ 0 ].getName().equals( "tree 0" ) ) {
3951 if ( !phylogenies[ 1 ].getName().equals( "tree 1" ) ) {
3954 if ( phylogenies[ 1 ].getNumberOfExternalNodes() != 10 ) {
3957 if ( phylogenies[ 2 ].getNumberOfExternalNodes() != 3 ) {
3960 if ( phylogenies[ 3 ].getNumberOfExternalNodes() != 3 ) {
3963 if ( phylogenies[ 4 ].getNumberOfExternalNodes() != 3 ) {
3966 if ( phylogenies[ 5 ].getNumberOfExternalNodes() != 3 ) {
3969 if ( phylogenies[ 6 ].getNumberOfExternalNodes() != 3 ) {
3972 if ( phylogenies[ 7 ].getNumberOfExternalNodes() != 3 ) {
3975 if ( !phylogenies[ 8 ].getName().equals( "tree 8" ) ) {
3978 if ( phylogenies[ 8 ].isRooted() ) {
3981 if ( phylogenies[ 8 ].getNumberOfExternalNodes() != 3 ) {
3984 if ( !phylogenies[ 9 ].getName().equals( "tree 9" ) ) {
3987 if ( !phylogenies[ 9 ].isRooted() ) {
3990 if ( phylogenies[ 9 ].getNumberOfExternalNodes() != 3 ) {
3993 if ( !phylogenies[ 10 ].getName().equals( "tree 10" ) ) {
3996 if ( !phylogenies[ 10 ].isRooted() ) {
3999 if ( phylogenies[ 10 ].getNumberOfExternalNodes() != 3 ) {
4002 if ( !phylogenies[ 11 ].getName().equals( "tree 11" ) ) {
4005 if ( phylogenies[ 11 ].isRooted() ) {
4008 if ( phylogenies[ 11 ].getNumberOfExternalNodes() != 3 ) {
4011 if ( !phylogenies[ 12 ].getName().equals( "tree 12" ) ) {
4014 if ( !phylogenies[ 12 ].isRooted() ) {
4017 if ( phylogenies[ 12 ].getNumberOfExternalNodes() != 3 ) {
4020 if ( !phylogenies[ 13 ].getName().equals( "tree 13" ) ) {
4023 if ( !phylogenies[ 13 ].isRooted() ) {
4026 if ( phylogenies[ 13 ].getNumberOfExternalNodes() != 3 ) {
4029 if ( !phylogenies[ 14 ].getName().equals( "tree 14" ) ) {
4032 if ( !phylogenies[ 14 ].isRooted() ) {
4035 if ( phylogenies[ 14 ].getNumberOfExternalNodes() != 10 ) {
4038 if ( !phylogenies[ 15 ].getName().equals( "tree 15" ) ) {
4041 if ( phylogenies[ 15 ].isRooted() ) {
4044 if ( phylogenies[ 15 ].getNumberOfExternalNodes() != 10 ) {
4047 if ( !phylogenies[ 16 ].getName().equals( "tree 16" ) ) {
4050 if ( !phylogenies[ 16 ].isRooted() ) {
4053 if ( phylogenies[ 16 ].getNumberOfExternalNodes() != 10 ) {
4056 if ( !phylogenies[ 17 ].getName().equals( "tree 17" ) ) {
4059 if ( phylogenies[ 17 ].isRooted() ) {
4062 if ( phylogenies[ 17 ].getNumberOfExternalNodes() != 10 ) {
4066 catch ( final Exception e ) {
4067 e.printStackTrace( System.out );
4073 private static boolean testNexusTreeParsingTranslating() {
4075 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
4076 final NexusPhylogeniesParser parser = new NexusPhylogeniesParser();
4077 Phylogeny[] phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_5.nex", parser );
4078 if ( phylogenies.length != 1 ) {
4081 if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 3 ) {
4084 if ( !phylogenies[ 0 ].getName().equals( "Tree0" ) ) {
4087 if ( !phylogenies[ 0 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
4090 if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
4093 if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
4094 .equals( "Aranaeus" ) ) {
4098 phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_6.nex", parser );
4099 if ( phylogenies.length != 3 ) {
4102 if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 3 ) {
4105 if ( !phylogenies[ 0 ].getName().equals( "Tree0" ) ) {
4108 if ( phylogenies[ 0 ].isRooted() ) {
4111 if ( !phylogenies[ 0 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
4114 if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
4117 if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
4118 .equals( "Aranaeus" ) ) {
4121 if ( phylogenies[ 1 ].getNumberOfExternalNodes() != 3 ) {
4124 if ( !phylogenies[ 1 ].getName().equals( "Tree1" ) ) {
4127 if ( phylogenies[ 1 ].isRooted() ) {
4130 if ( !phylogenies[ 1 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
4133 if ( !phylogenies[ 1 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
4136 if ( !phylogenies[ 1 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
4137 .equals( "Aranaeus" ) ) {
4140 if ( phylogenies[ 2 ].getNumberOfExternalNodes() != 3 ) {
4143 if ( !phylogenies[ 2 ].getName().equals( "Tree2" ) ) {
4146 if ( !phylogenies[ 2 ].isRooted() ) {
4149 if ( !phylogenies[ 2 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
4152 if ( !phylogenies[ 2 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
4155 if ( !phylogenies[ 2 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
4156 .equals( "Aranaeus" ) ) {
4160 phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_7.nex", parser );
4161 if ( phylogenies.length != 3 ) {
4164 if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 3 ) {
4167 if ( !phylogenies[ 0 ].getName().equals( "Tree0" ) ) {
4170 if ( phylogenies[ 0 ].isRooted() ) {
4173 if ( !phylogenies[ 0 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
4176 if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
4179 if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
4180 .equals( "Aranaeus" ) ) {
4183 if ( phylogenies[ 1 ].getNumberOfExternalNodes() != 3 ) {
4186 if ( !phylogenies[ 1 ].getName().equals( "Tree1" ) ) {
4189 if ( phylogenies[ 1 ].isRooted() ) {
4192 if ( !phylogenies[ 1 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
4195 if ( !phylogenies[ 1 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
4198 if ( !phylogenies[ 1 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
4199 .equals( "Aranaeus" ) ) {
4202 if ( phylogenies[ 2 ].getNumberOfExternalNodes() != 3 ) {
4205 if ( !phylogenies[ 2 ].getName().equals( "Tree2" ) ) {
4208 if ( !phylogenies[ 2 ].isRooted() ) {
4211 if ( !phylogenies[ 2 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
4214 if ( !phylogenies[ 2 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
4217 if ( !phylogenies[ 2 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
4218 .equals( "Aranaeus" ) ) {
4222 catch ( final Exception e ) {
4223 e.printStackTrace( System.out );
4229 private static boolean testNHParsing() {
4231 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
4232 final Phylogeny p1 = factory.create( "(A,B1)", new NHXParser() )[ 0 ];
4233 if ( !p1.toNewHampshireX().equals( "(A,B1)" ) ) {
4236 final NHXParser nhxp = new NHXParser();
4237 nhxp.setTaxonomyExtraction( PhylogenyMethods.TAXONOMY_EXTRACTION.NO );
4238 nhxp.setReplaceUnderscores( true );
4239 final Phylogeny uc0 = factory.create( "(A__A_,_B_B)", nhxp )[ 0 ];
4240 if ( !uc0.getRoot().getChildNode( 0 ).getName().equals( "A A " ) ) {
4243 if ( !uc0.getRoot().getChildNode( 1 ).getName().equals( " B B" ) ) {
4246 final Phylogeny p1b = factory
4247 .create( " \n \t \b \r \f ; ( \n \t \b \r \f; A ; \n \t \b \r \f, \n \t \b \r \f; B ; \n \t \b \r \f 1 \n \t \b \r \f ; \n \t \b \r \f );;;;; \n \t \b \r \f;;; \n \t \b \r \f ",
4248 new NHXParser() )[ 0 ];
4249 if ( !p1b.toNewHampshireX().equals( "(';A;',';B;1;')" ) ) {
4252 if ( !p1b.toNewHampshire().equals( "(';A;',';B;1;');" ) ) {
4255 final Phylogeny p2 = factory.create( new StringBuffer( "(A,B2)" ), new NHXParser() )[ 0 ];
4256 final Phylogeny p3 = factory.create( new char[] { '(', 'A', ',', 'B', '3', ')' }, new NHXParser() )[ 0 ];
4257 final Phylogeny p4 = factory.create( "(A,B4);", new NHXParser() )[ 0 ];
4258 final Phylogeny p5 = factory.create( new StringBuffer( "(A,B5);" ), new NHXParser() )[ 0 ];
4259 final Phylogeny[] p7 = factory.create( "(A,B7);(C,D7)", new NHXParser() );
4260 final Phylogeny[] p8 = factory.create( "(A,B8) (C,D8)", new NHXParser() );
4261 final Phylogeny[] p9 = factory.create( "(A,B9)\n(C,D9)", new NHXParser() );
4262 final Phylogeny[] p10 = factory.create( "(A,B10);(C,D10);", new NHXParser() );
4263 final Phylogeny[] p11 = factory.create( "(A,B11);(C,D11) (E,F11)\t(G,H11)", new NHXParser() );
4264 final Phylogeny[] p12 = factory.create( "(A,B12) (C,D12) (E,F12) (G,H12)", new NHXParser() );
4265 final Phylogeny[] p13 = factory.create( " ; (;A; , ; B ; 1 3 ; \n)\t ( \n ;"
4266 + " C ; ,; D;13;);;;;;;(;E;,;F;13 ;) ; "
4267 + "; ; ( \t\n\r\b; G ;, ;H ;1 3; ) ; ; ;",
4269 if ( !p13[ 0 ].toNewHampshireX().equals( "(';A;',';B;13;')" ) ) {
4272 if ( !p13[ 1 ].toNewHampshireX().equals( "(';C;',';D;13;')" ) ) {
4275 if ( !p13[ 2 ].toNewHampshireX().equals( "(';E;',';F;13;')" ) ) {
4278 if ( !p13[ 3 ].toNewHampshireX().equals( "(';G;',';H;13;')" ) ) {
4281 final Phylogeny[] p14 = factory.create( "(A,B14)ab", new NHXParser() );
4282 final Phylogeny[] p15 = factory.create( "(A,B15)ab;", new NHXParser() );
4283 final String p16_S = "((A,B),C)";
4284 final Phylogeny[] p16 = factory.create( p16_S, new NHXParser() );
4285 if ( !p16[ 0 ].toNewHampshireX().equals( p16_S ) ) {
4288 final String p17_S = "(C,(A,B))";
4289 final Phylogeny[] p17 = factory.create( p17_S, new NHXParser() );
4290 if ( !p17[ 0 ].toNewHampshireX().equals( p17_S ) ) {
4293 final String p18_S = "((A,B),(C,D))";
4294 final Phylogeny[] p18 = factory.create( p18_S, new NHXParser() );
4295 if ( !p18[ 0 ].toNewHampshireX().equals( p18_S ) ) {
4298 final String p19_S = "(((A,B),C),D)";
4299 final Phylogeny[] p19 = factory.create( p19_S, new NHXParser() );
4300 if ( !p19[ 0 ].toNewHampshireX().equals( p19_S ) ) {
4303 final String p20_S = "(A,(B,(C,D)))";
4304 final Phylogeny[] p20 = factory.create( p20_S, new NHXParser() );
4305 if ( !p20[ 0 ].toNewHampshireX().equals( p20_S ) ) {
4308 final String p21_S = "(A,(B,(C,(D,E))))";
4309 final Phylogeny[] p21 = factory.create( p21_S, new NHXParser() );
4310 if ( !p21[ 0 ].toNewHampshireX().equals( p21_S ) ) {
4313 final String p22_S = "((((A,B),C),D),E)";
4314 final Phylogeny[] p22 = factory.create( p22_S, new NHXParser() );
4315 if ( !p22[ 0 ].toNewHampshireX().equals( p22_S ) ) {
4318 final String p23_S = "(A,(B,(C,(D,E)de)cde)bcde)abcde";
4319 final Phylogeny[] p23 = factory.create( p23_S, new NHXParser() );
4320 if ( !p23[ 0 ].toNewHampshireX().equals( p23_S ) ) {
4323 final String p24_S = "((((A,B)ab,C)abc,D)abcd,E)abcde";
4324 final Phylogeny[] p24 = factory.create( p24_S, new NHXParser() );
4325 if ( !p24[ 0 ].toNewHampshireX().equals( p24_S ) ) {
4328 final String p241_S1 = "(A,(B,(C,(D,E)de)cde)bcde)abcde";
4329 final String p241_S2 = "((((A,B)ab,C)abc,D)abcd,E)abcde";
4330 final Phylogeny[] p241 = factory.create( p241_S1 + p241_S2, new NHXParser() );
4331 if ( !p241[ 0 ].toNewHampshireX().equals( p241_S1 ) ) {
4334 if ( !p241[ 1 ].toNewHampshireX().equals( p241_S2 ) ) {
4337 final String p25_S = "((((((((((((((A,B)ab,C)abc,D)abcd,E)"
4338 + "abcde,(B,(C,(D,E)de)cde)bcde)abcde,(B,((A,(B,(C,(D,"
4339 + "E)de)cde)bcde)abcde,(D,E)de)cde)bcde)abcde,B)ab,C)"
4340 + "abc,((((A,B)ab,C)abc,D)abcd,E)abcde)abcd,E)abcde,"
4341 + "((((A,((((((((A,B)ab,C)abc,((((A,B)ab,C)abc,D)abcd,"
4342 + "E)abcde)abcd,E)abcde,((((A,B)ab,C)abc,D)abcd,E)abcde)"
4343 + "ab,C)abc,((((A,B)ab,C)abc,D)abcd,E)abcde)abcd,E)abcde"
4344 + ")ab,C)abc,D)abcd,E)abcde)ab,C)abc,((((A,B)ab,C)abc,D)" + "abcd,E)abcde)abcd,E)abcde";
4345 final Phylogeny[] p25 = factory.create( p25_S, new NHXParser() );
4346 if ( !p25[ 0 ].toNewHampshireX().equals( p25_S ) ) {
4349 final String p26_S = "(A,B)ab";
4350 final Phylogeny[] p26 = factory.create( p26_S, new NHXParser() );
4351 if ( !p26[ 0 ].toNewHampshireX().equals( p26_S ) ) {
4354 final String p27_S = "((((A,B)ab,C)abc,D)abcd,E)abcde";
4355 final Phylogeny[] p27 = factory.create( new File( Test.PATH_TO_TEST_DATA + "phylogeny27.nhx" ),
4357 if ( !p27[ 0 ].toNewHampshireX().equals( p27_S ) ) {
4360 final String p28_S1 = "((((A,B)ab,C)abc,D)abcd,E)abcde";
4361 final String p28_S2 = "(A,(B,(C,(D,E)de)cde)bcde)abcde";
4362 final String p28_S3 = "(A,B)ab";
4363 final String p28_S4 = "((((A,B),C),D),;E;)";
4364 final Phylogeny[] p28 = factory.create( new File( Test.PATH_TO_TEST_DATA + "phylogeny28.nhx" ),
4366 if ( !p28[ 0 ].toNewHampshireX().equals( p28_S1 ) ) {
4369 if ( !p28[ 1 ].toNewHampshireX().equals( p28_S2 ) ) {
4372 if ( !p28[ 2 ].toNewHampshireX().equals( p28_S3 ) ) {
4375 if ( !p28[ 3 ].toNewHampshireX().equals( "((((A,B),C),D),';E;')" ) ) {
4378 final String p29_S = "((((A:0.01,B:0.684)ab:0.345,C:0.3451)abc:0.3451,D:1.5)abcd:0.134,E:0.32)abcde:0.1345";
4379 final Phylogeny[] p29 = factory.create( p29_S, new NHXParser() );
4380 if ( !p29[ 0 ].toNewHampshireX().equals( p29_S ) ) {
4383 final String p30_S = "((((A:0.01,B:0.02):0.93,C:0.04):0.05,D:1.4):0.06,E):0.72";
4384 final Phylogeny[] p30 = factory.create( p30_S, new NHXParser() );
4385 if ( !p30[ 0 ].toNewHampshireX().equals( p30_S ) ) {
4388 final String p32_S = " ; ; \n \t \b \f \r ;;;;;; ";
4389 final Phylogeny[] p32 = factory.create( p32_S, new NHXParser() );
4390 if ( ( p32.length != 1 ) || !p32[ 0 ].isEmpty() ) {
4393 final String p33_S = "A";
4394 final Phylogeny[] p33 = factory.create( p33_S, new NHXParser() );
4395 if ( !p33[ 0 ].toNewHampshireX().equals( p33_S ) ) {
4398 final String p34_S = "B;";
4399 final Phylogeny[] p34 = factory.create( p34_S, new NHXParser() );
4400 if ( !p34[ 0 ].toNewHampshireX().equals( "B" ) ) {
4403 final String p35_S = "B:0.2";
4404 final Phylogeny[] p35 = factory.create( p35_S, new NHXParser() );
4405 if ( !p35[ 0 ].toNewHampshireX().equals( p35_S ) ) {
4408 final String p36_S = "(A)";
4409 final Phylogeny[] p36 = factory.create( p36_S, new NHXParser() );
4410 if ( !p36[ 0 ].toNewHampshireX().equals( p36_S ) ) {
4413 final String p37_S = "((A))";
4414 final Phylogeny[] p37 = factory.create( p37_S, new NHXParser() );
4415 if ( !p37[ 0 ].toNewHampshireX().equals( p37_S ) ) {
4418 final String p38_S = "(((((((A:0.2):0.2):0.3):0.4):0.5):0.6):0.7):0.8";
4419 final Phylogeny[] p38 = factory.create( p38_S, new NHXParser() );
4420 if ( !p38[ 0 ].toNewHampshireX().equals( p38_S ) ) {
4423 final String p39_S = "(((B,((((A:0.2):0.2):0.3):0.4):0.5):0.6):0.7):0.8";
4424 final Phylogeny[] p39 = factory.create( p39_S, new NHXParser() );
4425 if ( !p39[ 0 ].toNewHampshireX().equals( p39_S ) ) {
4428 final String p40_S = "(A,B,C)";
4429 final Phylogeny[] p40 = factory.create( p40_S, new NHXParser() );
4430 if ( !p40[ 0 ].toNewHampshireX().equals( p40_S ) ) {
4433 final String p41_S = "(A,B,C,D,E,F,G,H,I,J,K)";
4434 final Phylogeny[] p41 = factory.create( p41_S, new NHXParser() );
4435 if ( !p41[ 0 ].toNewHampshireX().equals( p41_S ) ) {
4438 final String p42_S = "(A,B,(X,Y,Z),D,E,F,G,H,I,J,K)";
4439 final Phylogeny[] p42 = factory.create( p42_S, new NHXParser() );
4440 if ( !p42[ 0 ].toNewHampshireX().equals( p42_S ) ) {
4443 final String p43_S = "(A,B,C,(AA,BB,CC,(CCC,DDD,EEE,(FFFF,GGGG)x)y,DD,EE,FF,GG,HH),D,E,(EE,FF),F,G,H,(((((5)4)3)2)1),I,J,K,L,M,N,O,P,Q,R,S,T,U,V,W,X,(XX,(YY)),Y,Z)";
4444 final Phylogeny[] p43 = factory.create( p43_S, new NHXParser() );
4445 if ( !p43[ 0 ].toNewHampshireX().equals( p43_S ) ) {
4448 final String p44_S = "(((A,B,C,D),(A,B,C,D),(A,B,C,D),(A,B,C,D)),((A,B,C,D),(A,B,C,D),(A,B,C,D),(A,B,C,D)),((A,B,C,D),(A,B,C,D),(A,B,C,D),(A,B,C,D)),((A,B,C,D),(A,B,C,D),(A,B,C,D),(A,B,C,D)))";
4449 final Phylogeny[] p44 = factory.create( p44_S, new NHXParser() );
4450 if ( !p44[ 0 ].toNewHampshireX().equals( p44_S ) ) {
4453 final String p45_S = "((((((((((A))))))))),(((((((((B))))))))),(((((((((C))))))))))";
4454 final Phylogeny[] p45 = factory.create( p45_S, new NHXParser() );
4455 if ( !p45[ 0 ].toNewHampshireX().equals( p45_S ) ) {
4458 final String p46_S = "";
4459 final Phylogeny[] p46 = factory.create( p46_S, new NHXParser() );
4460 if ( ( p46.length != 1 ) || !p46[ 0 ].isEmpty() ) {
4463 final Phylogeny p47 = factory.create( new StringBuffer( "((A,B)ab:2[0.44],C)" ), new NHXParser() )[ 0 ];
4464 if ( !isEqual( 0.44, p47.getNode( "ab" ).getBranchData().getConfidence( 0 ).getValue() ) ) {
4467 final Phylogeny p48 = factory.create( new StringBuffer( "((A,B)ab:2[88],C)" ), new NHXParser() )[ 0 ];
4468 if ( !isEqual( 88, p48.getNode( "ab" ).getBranchData().getConfidence( 0 ).getValue() ) ) {
4471 final Phylogeny p49 = factory
4472 .create( new StringBuffer( "((A,B)a[comment:a,b;(a)]b:2[0.44][comment(a,b,b);],C)" ),
4473 new NHXParser() )[ 0 ];
4474 if ( !isEqual( 0.44, p49.getNode( "ab" ).getBranchData().getConfidence( 0 ).getValue() ) ) {
4477 final Phylogeny p50 = factory.create( new StringBuffer( "((\"A\",B)ab:2[88],C)" ), new NHXParser() )[ 0 ];
4478 if ( p50.getNode( "A" ) == null ) {
4481 if ( !p50.toNewHampshire( false, NH_CONVERSION_SUPPORT_VALUE_STYLE.IN_SQUARE_BRACKETS )
4482 .equals( "((A,B)ab:2.0[88],C);" ) ) {
4485 if ( !p50.toNewHampshire( false, NH_CONVERSION_SUPPORT_VALUE_STYLE.NONE ).equals( "((A,B)ab:2.0,C);" ) ) {
4488 if ( !p50.toNewHampshire( false, NH_CONVERSION_SUPPORT_VALUE_STYLE.AS_INTERNAL_NODE_NAMES )
4489 .equals( "((A,B)88:2.0,C);" ) ) {
4492 final Phylogeny p51 = factory.create( new StringBuffer( "((\"A(A\",B)ab:2[88],C)" ), new NHXParser() )[ 0 ];
4493 if ( p51.getNode( "A(A" ) == null ) {
4496 final Phylogeny p52 = factory.create( new StringBuffer( "(('A(A',B)ab:2[88],C)" ), new NHXParser() )[ 0 ];
4497 if ( p52.getNode( "A(A" ) == null ) {
4500 final Phylogeny p53 = factory
4501 .create( new StringBuffer( "(('A(A',\"B (x (a' ,b) f(x);\"[com])[ment]ab:2[88],C)" ),
4502 new NHXParser() )[ 0 ];
4503 if ( p53.getNode( "B (x (a' ,b) f(x);" ) == null ) {
4507 final Phylogeny p54 = factory.create( new StringBuffer( "((A,B):[88],C)" ), new NHXParser() )[ 0 ];
4508 if ( p54.getNode( "A" ) == null ) {
4511 if ( !p54.toNewHampshire( false, NH_CONVERSION_SUPPORT_VALUE_STYLE.IN_SQUARE_BRACKETS )
4512 .equals( "((A,B)[88],C);" ) ) {
4516 catch ( final Exception e ) {
4517 e.printStackTrace( System.out );
4523 private static boolean testNHXconversion() {
4525 final PhylogenyNode n1 = new PhylogenyNode();
4526 final PhylogenyNode n2 = PhylogenyNode.createInstanceFromNhxString( "" );
4527 final PhylogenyNode n3 = PhylogenyNode.createInstanceFromNhxString( "n3" );
4528 final PhylogenyNode n4 = PhylogenyNode.createInstanceFromNhxString( "n4:0.01" );
4529 final PhylogenyNode n5 = PhylogenyNode
4530 .createInstanceFromNhxString( "n5:0.1[&&NHX:S=Ecoli:E=1.1.1.1:D=Y:Co=Y:B=56:T=1:W=2:C=10.20.30:XN=S=tag1=value1=unit1]" );
4531 final PhylogenyNode n6 = PhylogenyNode
4532 .createInstanceFromNhxString( "n6:0.000001[&&NHX:S=Ecoli:E=1.1.1.1:D=N:Co=N:B=100:T=1:W=2:C=0.0.0:XN=B=bool_tag=T]" );
4533 if ( !n1.toNewHampshireX().equals( "" ) ) {
4536 if ( !n2.toNewHampshireX().equals( "" ) ) {
4539 if ( !n3.toNewHampshireX().equals( "n3" ) ) {
4542 if ( !n4.toNewHampshireX().equals( "n4:0.01" ) ) {
4545 if ( !n5.toNewHampshireX()
4546 .equals( "n5:0.1[&&NHX:T=1:S=Ecoli:D=Y:XN=S=tag1=value1=unit1:B=56:W=2.0:C=10.20.30]" ) ) {
4549 if ( !n6.toNewHampshireX().equals( "n6:1.0E-6[&&NHX:T=1:S=Ecoli:D=N:XN=B=bool_tag=T:B=100:W=2.0:C=0.0.0]" ) ) {
4553 catch ( final Exception e ) {
4554 e.printStackTrace( System.out );
4560 private static boolean testNHXNodeParsing() {
4562 final PhylogenyNode n1 = new PhylogenyNode();
4563 final PhylogenyNode n2 = PhylogenyNode.createInstanceFromNhxString( "" );
4564 final PhylogenyNode n3 = PhylogenyNode.createInstanceFromNhxString( "n3" );
4565 final PhylogenyNode n4 = PhylogenyNode.createInstanceFromNhxString( "n4:0.01" );
4566 final PhylogenyNode n5 = PhylogenyNode
4567 .createInstanceFromNhxString( "n5:0.1[&&NHX:S=Ecoli:E=1.1.1.1:D=Y:B=56:T=1:On=22:SOn=33:SNn=44:W=2:C=10.20.30:XN=S=tag1=value1=unit1:XN=S=tag3=value3=unit3]" );
4568 if ( !n3.getName().equals( "n3" ) ) {
4571 if ( n3.getDistanceToParent() != PhylogenyDataUtil.BRANCH_LENGTH_DEFAULT ) {
4574 if ( n3.isDuplication() ) {
4577 if ( n3.isHasAssignedEvent() ) {
4580 if ( PhylogenyMethods.getBranchWidthValue( n3 ) != BranchWidth.BRANCH_WIDTH_DEFAULT_VALUE ) {
4583 if ( !n4.getName().equals( "n4" ) ) {
4586 if ( n4.getDistanceToParent() != 0.01 ) {
4589 if ( !n5.getName().equals( "n5" ) ) {
4592 if ( PhylogenyMethods.getConfidenceValue( n5 ) != 56 ) {
4595 if ( n5.getDistanceToParent() != 0.1 ) {
4598 if ( !PhylogenyMethods.getSpecies( n5 ).equals( "Ecoli" ) ) {
4601 if ( !n5.isDuplication() ) {
4604 if ( !n5.isHasAssignedEvent() ) {
4607 if ( PhylogenyMethods.getBranchWidthValue( n5 ) != 2 ) {
4610 if ( n5.getNodeData().getProperties().getPropertyRefs().length != 2 ) {
4613 final PhylogenyNode n8 = PhylogenyNode
4614 .createInstanceFromNhxString( "n8_ECOLI/12:0.01",
4615 PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4616 if ( !n8.getName().equals( "n8_ECOLI/12" ) ) {
4619 if ( !PhylogenyMethods.getSpecies( n8 ).equals( "ECOLI" ) ) {
4622 final PhylogenyNode n9 = PhylogenyNode
4623 .createInstanceFromNhxString( "n9_ECOLI/12=12:0.01",
4624 PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4625 if ( !n9.getName().equals( "n9_ECOLI/12=12" ) ) {
4628 if ( !PhylogenyMethods.getSpecies( n9 ).equals( "ECOLI" ) ) {
4631 final PhylogenyNode n10 = PhylogenyNode
4632 .createInstanceFromNhxString( "n10.ECOLI", PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4633 if ( !n10.getName().equals( "n10.ECOLI" ) ) {
4636 final PhylogenyNode n20 = PhylogenyNode
4637 .createInstanceFromNhxString( "n20_ECOLI/1-2", PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4638 if ( !n20.getName().equals( "n20_ECOLI/1-2" ) ) {
4641 if ( !PhylogenyMethods.getSpecies( n20 ).equals( "ECOLI" ) ) {
4644 final PhylogenyNode n20x = PhylogenyNode
4645 .createInstanceFromNhxString( "n20_ECOL1/1-2", PhylogenyMethods.TAXONOMY_EXTRACTION.YES );
4646 if ( !n20x.getName().equals( "n20_ECOL1/1-2" ) ) {
4649 if ( !PhylogenyMethods.getSpecies( n20x ).equals( "ECOL1" ) ) {
4652 final PhylogenyNode n20xx = PhylogenyNode
4653 .createInstanceFromNhxString( "n20_eCOL1/1-2", PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4654 if ( !n20xx.getName().equals( "n20_eCOL1/1-2" ) ) {
4657 if ( PhylogenyMethods.getSpecies( n20xx ).length() > 0 ) {
4660 final PhylogenyNode n20xxx = PhylogenyNode
4661 .createInstanceFromNhxString( "n20_ecoli/1-2", PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4662 if ( !n20xxx.getName().equals( "n20_ecoli/1-2" ) ) {
4665 if ( PhylogenyMethods.getSpecies( n20xxx ).length() > 0 ) {
4668 final PhylogenyNode n20xxxx = PhylogenyNode
4669 .createInstanceFromNhxString( "n20_Ecoli/1-2", PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4670 if ( !n20xxxx.getName().equals( "n20_Ecoli/1-2" ) ) {
4673 if ( PhylogenyMethods.getSpecies( n20xxxx ).length() > 0 ) {
4676 final PhylogenyNode n21 = PhylogenyNode
4677 .createInstanceFromNhxString( "n21_PIG", PhylogenyMethods.TAXONOMY_EXTRACTION.YES );
4678 if ( !n21.getName().equals( "n21_PIG" ) ) {
4681 if ( !PhylogenyMethods.getSpecies( n21 ).equals( "PIG" ) ) {
4684 final PhylogenyNode n21x = PhylogenyNode
4685 .createInstanceFromNhxString( "n21_PIG", PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4686 if ( !n21x.getName().equals( "n21_PIG" ) ) {
4689 if ( PhylogenyMethods.getSpecies( n21x ).length() > 0 ) {
4692 final PhylogenyNode n22 = PhylogenyNode
4693 .createInstanceFromNhxString( "n22/PIG", PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4694 if ( !n22.getName().equals( "n22/PIG" ) ) {
4697 if ( PhylogenyMethods.getSpecies( n22 ).length() > 0 ) {
4700 final PhylogenyNode n23 = PhylogenyNode
4701 .createInstanceFromNhxString( "n23/PIG_1", PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4702 if ( !n23.getName().equals( "n23/PIG_1" ) ) {
4705 if ( PhylogenyMethods.getSpecies( n23 ).length() > 0 ) {
4708 if ( NHXParser.LIMIT_SPECIES_NAMES_TO_FIVE_CHARS ) {
4709 final PhylogenyNode a = PhylogenyNode
4710 .createInstanceFromNhxString( "n10_ECOLI/1-2",
4711 PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4712 if ( !a.getName().equals( "n10_ECOLI/1-2" ) ) {
4715 if ( !PhylogenyMethods.getSpecies( a ).equals( "ECOLI" ) ) {
4718 final PhylogenyNode b = PhylogenyNode
4719 .createInstanceFromNhxString( "n10_ECOLI1/1-2",
4720 PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4721 if ( !b.getName().equals( "n10_ECOLI1/1-2" ) ) {
4724 if ( !PhylogenyMethods.getSpecies( b ).equals( "" ) ) {
4727 final PhylogenyNode c = PhylogenyNode
4728 .createInstanceFromNhxString( "n10_RATAF12/1000-2000",
4729 PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4730 if ( !c.getName().equals( "n10_RATAF12/1000-2000" ) ) {
4733 if ( !PhylogenyMethods.getSpecies( c ).equals( "" ) ) {
4736 final PhylogenyNode c1 = PhylogenyNode
4737 .createInstanceFromNhxString( "n10_BOVIN_1/1000-2000",
4738 PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4739 if ( !c1.getName().equals( "n10_BOVIN_1/1000-2000" ) ) {
4742 if ( !PhylogenyMethods.getSpecies( c1 ).equals( "BOVIN" ) ) {
4745 final PhylogenyNode c2 = PhylogenyNode
4746 .createInstanceFromNhxString( "n10_Bovin_1/1000-2000",
4747 PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4748 if ( !c2.getName().equals( "n10_Bovin_1/1000-2000" ) ) {
4751 if ( !PhylogenyMethods.getSpecies( c2 ).equals( "" ) ) {
4754 final PhylogenyNode d = PhylogenyNode
4755 .createInstanceFromNhxString( "n10_RAT1/1-2",
4756 PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4757 if ( !d.getName().equals( "n10_RAT1/1-2" ) ) {
4760 if ( !PhylogenyMethods.getSpecies( d ).equals( "RAT" ) ) {
4763 final PhylogenyNode e = PhylogenyNode
4764 .createInstanceFromNhxString( "n10_RAT1", PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4765 if ( !e.getName().equals( "n10_RAT1" ) ) {
4768 if ( !ForesterUtil.isEmpty( PhylogenyMethods.getSpecies( e ) ) ) {
4772 final PhylogenyNode n11 = PhylogenyNode
4773 .createInstanceFromNhxString( "n111111_ECOLI/jdj:0.4",
4774 PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4775 if ( !n11.getName().equals( "n111111_ECOLI/jdj" ) ) {
4778 if ( n11.getDistanceToParent() != 0.4 ) {
4781 if ( !PhylogenyMethods.getSpecies( n11 ).equals( "ECOLI" ) ) {
4784 final PhylogenyNode n12 = PhylogenyNode
4785 .createInstanceFromNhxString( "n111111-ECOLI---/jdj:0.4",
4786 PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4787 if ( !n12.getName().equals( "n111111-ECOLI---/jdj" ) ) {
4790 if ( n12.getDistanceToParent() != 0.4 ) {
4793 if ( PhylogenyMethods.getSpecies( n12 ).length() > 0 ) {
4796 final Property tvu1 = n5.getNodeData().getProperties().getProperty( "tag1" );
4797 final Property tvu3 = n5.getNodeData().getProperties().getProperty( "tag3" );
4798 if ( !tvu1.getRef().equals( "tag1" ) ) {
4801 if ( !tvu1.getDataType().equals( "xsd:string" ) ) {
4804 if ( !tvu1.getUnit().equals( "unit1" ) ) {
4807 if ( !tvu1.getValue().equals( "value1" ) ) {
4810 if ( !tvu3.getRef().equals( "tag3" ) ) {
4813 if ( !tvu3.getDataType().equals( "xsd:string" ) ) {
4816 if ( !tvu3.getUnit().equals( "unit3" ) ) {
4819 if ( !tvu3.getValue().equals( "value3" ) ) {
4822 if ( n1.getName().compareTo( "" ) != 0 ) {
4825 if ( PhylogenyMethods.getConfidenceValue( n1 ) != Confidence.CONFIDENCE_DEFAULT_VALUE ) {
4828 if ( n1.getDistanceToParent() != PhylogenyDataUtil.BRANCH_LENGTH_DEFAULT ) {
4831 if ( n2.getName().compareTo( "" ) != 0 ) {
4834 if ( PhylogenyMethods.getConfidenceValue( n2 ) != Confidence.CONFIDENCE_DEFAULT_VALUE ) {
4837 if ( n2.getDistanceToParent() != PhylogenyDataUtil.BRANCH_LENGTH_DEFAULT ) {
4840 final PhylogenyNode n00 = PhylogenyNode
4841 .createInstanceFromNhxString( "n7:0.000001[&&NHX:GN=gene_name:AC=accession123:ID=node_identifier:S=Ecoli:D=N:Co=N:B=100:T=1:On=100:SOn=100:SNn=100:W=2:C=0.0.0:XN=U=url_tag=www.yahoo.com]" );
4842 if ( !n00.getNodeData().getNodeIdentifier().getValue().equals( "node_identifier" ) ) {
4845 if ( !n00.getNodeData().getSequence().getName().equals( "gene_name" ) ) {
4848 if ( !n00.getNodeData().getSequence().getAccession().getValue().equals( "accession123" ) ) {
4851 if ( !n00.getNodeData().getProperties().getProperty( "url_tag" ).getRef().equals( "url_tag" ) ) {
4854 if ( n00.getNodeData().getProperties().getProperty( "url_tag" ).getAppliesTo() != Property.AppliesTo.NODE ) {
4857 if ( !n00.getNodeData().getProperties().getProperty( "url_tag" ).getDataType().equals( "xsd:anyURI" ) ) {
4860 if ( !n00.getNodeData().getProperties().getProperty( "url_tag" ).getValue().equals( "www.yahoo.com" ) ) {
4863 if ( !n00.getNodeData().getProperties().getProperty( "url_tag" ).getUnit().equals( "" ) ) {
4866 final PhylogenyNode nx = PhylogenyNode.createInstanceFromNhxString( "n5:0.1[&&NHX:S=Ecoli:GN=gene_1]" );
4867 if ( !nx.getNodeData().getSequence().getName().equals( "gene_1" ) ) {
4870 final PhylogenyNode nx2 = PhylogenyNode.createInstanceFromNhxString( "n5:0.1[&&NHX:S=Ecoli:G=gene_2]" );
4871 if ( !nx2.getNodeData().getSequence().getName().equals( "gene_2" ) ) {
4874 final PhylogenyNode n13 = PhylogenyNode
4875 .createInstanceFromNhxString( "blah_12345/1-2",
4876 PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4877 if ( !n13.getName().equals( "blah_12345/1-2" ) ) {
4880 if ( !PhylogenyMethods.getSpecies( n13 ).equals( "" ) ) {
4883 final PhylogenyNode n14 = PhylogenyNode
4884 .createInstanceFromNhxString( "blah_12X45/1-2",
4885 PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4886 if ( !n14.getName().equals( "blah_12X45/1-2" ) ) {
4889 if ( !PhylogenyMethods.getSpecies( n14 ).equals( "12X45" ) ) {
4892 final PhylogenyNode n15 = PhylogenyNode
4893 .createInstanceFromNhxString( "something_wicked[123]",
4894 PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4895 if ( !n15.getName().equals( "something_wicked" ) ) {
4898 if ( n15.getBranchData().getNumberOfConfidences() != 1 ) {
4901 if ( !isEqual( n15.getBranchData().getConfidence( 0 ).getValue(), 123 ) ) {
4904 final PhylogenyNode n16 = PhylogenyNode
4905 .createInstanceFromNhxString( "something_wicked2[9]",
4906 PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4907 if ( !n16.getName().equals( "something_wicked2" ) ) {
4910 if ( n16.getBranchData().getNumberOfConfidences() != 1 ) {
4913 if ( !isEqual( n16.getBranchData().getConfidence( 0 ).getValue(), 9 ) ) {
4916 final PhylogenyNode n17 = PhylogenyNode
4917 .createInstanceFromNhxString( "something_wicked3[a]",
4918 PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4919 if ( !n17.getName().equals( "something_wicked3" ) ) {
4922 if ( n17.getBranchData().getNumberOfConfidences() != 0 ) {
4925 final PhylogenyNode n18 = PhylogenyNode
4926 .createInstanceFromNhxString( ":0.5[91]", PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4927 if ( !isEqual( n18.getDistanceToParent(), 0.5 ) ) {
4930 if ( n18.getBranchData().getNumberOfConfidences() != 1 ) {
4933 if ( !isEqual( n18.getBranchData().getConfidence( 0 ).getValue(), 91 ) ) {
4937 catch ( final Exception e ) {
4938 e.printStackTrace( System.out );
4944 private static boolean testNHXParsing() {
4946 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
4947 final Phylogeny p1 = factory.create( "(A [&&NHX:S=a_species],B1[&&NHX:S=b_species])", new NHXParser() )[ 0 ];
4948 if ( !p1.toNewHampshireX().equals( "(A[&&NHX:S=a_species],B1[&&NHX:S=b_species])" ) ) {
4951 final String p2_S = "(((((((A:0.2[&&NHX:S=qwerty]):0.2[&&NHX:S=uiop]):0.3[&&NHX:S=asdf]):0.4[&&NHX:S=zxc]):0.5[&&NHX:S=a]):0.6[&&NHX:S=asd]):0.7[&&NHX:S=za]):0.8[&&NHX:S=zaq]";
4952 final Phylogeny[] p2 = factory.create( p2_S, new NHXParser() );
4953 if ( !p2[ 0 ].toNewHampshireX().equals( p2_S ) ) {
4956 final String p2b_S = "(((((((A:0.2[&NHX:S=qw,erty]):0.2[&:S=u(io)p]):0.3[&NHX:S=asdf]):0.4[S=zxc]):0.5[]):0.6[&&NH:S=asd]):0.7[&&HX:S=za]):0.8[&&:S=zaq]";
4957 final Phylogeny[] p2b = factory.create( p2b_S, new NHXParser() );
4958 if ( !p2b[ 0 ].toNewHampshireX().equals( "(((((((A:0.2):0.2):0.3):0.4):0.5):0.6):0.7):0.8" ) ) {
4961 final Phylogeny[] p3 = factory
4962 .create( "[ comment&&NHX,())))](((((((A:0.2[&&NHX:S=qwerty]):0.2[&&NHX:S=uiop]):0.3[&&NHX:S=asdf]):0.4[&&NHX:S=zxc]):0.5[&&NHX:S=a]):0.6[&&NHX:S=asd]):0.7[&&NHX:S=za]):0.8[&&NHX:S=zaq]",
4964 if ( !p3[ 0 ].toNewHampshireX().equals( p2_S ) ) {
4967 final Phylogeny[] p4 = factory
4968 .create( "(((((((A:0.2[&&NHX:S=qwerty]):0.2[&&NHX:S=uiop]):0.3[&&NHX:S=asdf]):0.4[&&NHX:S=zxc]):0.5[&&NHX:S=a]):0.6[&&NHX:S=asd]):0.7[&&NHX:S=za]):0.8[&&NHX:S=zaq][comment(]",
4970 if ( !p4[ 0 ].toNewHampshireX().equals( p2_S ) ) {
4973 final Phylogeny[] p5 = factory
4974 .create( "[] ( [][ ][ ] ([((( &&NHXcomment only![[[[[[]([]((((A:0.2[&&NHX:S=q[comment )))]werty][,,,,))]):0.2[&&NHX:S=uiop]):0.3[&&NHX:S=a[comment,,))]sdf])[comment(((]:0.4[&&NHX:S=zxc][comment(((][comment(((]):0.5[&&NHX:S=a]):0.6[&&NHX:S=a[comment(((]sd]):0.7[&&NHX:S=za]):0.8[&&NHX:S=zaq][comment(((]",
4976 if ( !p5[ 0 ].toNewHampshireX().equals( p2_S ) ) {
4979 final String p6_S_C = "(A[][][][1][22][333][4444][55555][666666][&&NHX:S=Aspecies],B[))],C,(AA,BB,CC,(CCC,DDD,EEE,[comment](FFFF,GGGG)x)y,D[comment]D,EE,FF,GG,HH),D,E,(EE,FF),F,G,H,(((((5)4)3)2)1),I,J,K,L,M,N,O,P,Q,R,S,T,U,V,W,X,(XX,(YY)),Y,Z)";
4980 final String p6_S_WO_C = "(A[&&NHX:S=Aspecies],B,C,(AA,BB,CC,(CCC,DDD,EEE,(FFFF,GGGG)x)y,DD,EE,FF,GG,HH),D,E,(EE,FF),F,G,H,(((((5)4)3)2)1),I,J,K,L,M,N,O,P,Q,R,S,T,U,V,W,X,(XX,(YY)),Y,Z)";
4981 final Phylogeny[] p6 = factory.create( p6_S_C, new NHXParser() );
4982 if ( !p6[ 0 ].toNewHampshireX().equals( p6_S_WO_C ) ) {
4985 final String p7_S_C = "(((A [&&NHX:S=species_a], B [&&NHX:S=Vstorri] , C , D),(A,B,C,D[comment])[],[c][]([xxx]A[comment],[comment]B[comment][comment],[comment][comment]C[comment][comment],[comment][comment]D[comment][comment])[comment][comment],[comment] [comment](A,B,C,D)),((A,B,C,D),(A,B,C,D),(A,B,C,D),(A,B,C,D)),((A,B,C[comment][comment][comment][comment][comment] [comment],D),(A,B,C,D),(A,B,C,D),(A,B,C,D)),[comment][comment]((A,B,C,D),(A,B,C,D),(A,B,C,D),(A,B,C,D)))";
4986 final String p7_S_WO_C = "(((A[&&NHX:S=species_a],B[&&NHX:S=Vstorri],C,D),(A,B,C,D),(A,B,C,D),(A,B,C,D)),((A,B,C,D),(A,B,C,D),(A,B,C,D),(A,B,C,D)),((A,B,C,D),(A,B,C,D),(A,B,C,D),(A,B,C,D)),((A,B,C,D),(A,B,C,D),(A,B,C,D),(A,B,C,D)))";
4987 final Phylogeny[] p7 = factory.create( p7_S_C, new NHXParser() );
4988 if ( !p7[ 0 ].toNewHampshireX().equals( p7_S_WO_C ) ) {
4991 final String p8_S_C = "[cmt](((([]([))))))](((((A[&&NHX:S= [a comment] a])))))))[too many comments!:)])),(((((((((B[&&NHX[ a comment in a bad place]:S =b])))))[] [] )))),(((((((((C[&&NHX:S=c]) ))[,,, ])))))))";
4992 final String p8_S_WO_C = "((((((((((A[&&NHX:S=a]))))))))),(((((((((B[&&NHX:S=b]))))))))),(((((((((C[&&NHX:S=c]))))))))))";
4993 final Phylogeny[] p8 = factory.create( p8_S_C, new NHXParser() );
4994 if ( !p8[ 0 ].toNewHampshireX().equals( p8_S_WO_C ) ) {
4997 final Phylogeny p9 = factory.create( "((A:0.2,B:0.3):0.5[91],C:0.1)root:0.1[100]", new NHXParser() )[ 0 ];
4998 if ( !p9.toNewHampshireX().equals( "((A:0.2,B:0.3):0.5[&&NHX:B=91],C:0.1)root:0.1[&&NHX:B=100]" ) ) {
5001 final Phylogeny p10 = factory
5002 .create( " [79] ( (A [co mment] :0 .2[comment],B:0.3[com])[com ment]: 0. 5 \t[ 9 1 ][ comment],C: 0.1)[comment]root:0.1[100] [comment]",
5003 new NHXParser() )[ 0 ];
5004 if ( !p10.toNewHampshireX().equals( "((A:0.2,B:0.3):0.5[&&NHX:B=91],C:0.1)root:0.1[&&NHX:B=100]" ) ) {
5008 catch ( final Exception e ) {
5009 e.printStackTrace( System.out );
5015 private static boolean testNHXParsingQuotes() {
5017 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
5018 final NHXParser p = new NHXParser();
5019 final Phylogeny[] phylogenies_0 = factory.create( new File( Test.PATH_TO_TEST_DATA + "quotes.nhx" ), p );
5020 if ( phylogenies_0.length != 5 ) {
5023 final Phylogeny phy = phylogenies_0[ 4 ];
5024 if ( phy.getNumberOfExternalNodes() != 7 ) {
5027 if ( phy.getNodes( "a name in double quotes from tree ((a,b),c)" ).size() != 1 ) {
5030 if ( phy.getNodes( "charles darwin 'origin of species'" ).size() != 1 ) {
5033 if ( !phy.getNodes( "charles darwin 'origin of species'" ).get( 0 ).getNodeData().getTaxonomy()
5034 .getScientificName().equals( "hsapiens" ) ) {
5037 if ( phy.getNodes( "shouldbetogether single quotes" ).size() != 1 ) {
5040 if ( phy.getNodes( "'single quotes' inside double quotes" ).size() != 1 ) {
5043 if ( phy.getNodes( "double quotes inside single quotes" ).size() != 1 ) {
5046 if ( phy.getNodes( "noquotes" ).size() != 1 ) {
5049 if ( phy.getNodes( "A ( B C '" ).size() != 1 ) {
5052 final NHXParser p1p = new NHXParser();
5053 p1p.setIgnoreQuotes( true );
5054 final Phylogeny p1 = factory.create( "(\"A\",'B1')", p1p )[ 0 ];
5055 if ( !p1.toNewHampshire().equals( "(A,B1);" ) ) {
5058 final NHXParser p2p = new NHXParser();
5059 p1p.setIgnoreQuotes( false );
5060 final Phylogeny p2 = factory.create( "(\"A\",'B1')", p2p )[ 0 ];
5061 if ( !p2.toNewHampshire().equals( "(A,B1);" ) ) {
5064 final NHXParser p3p = new NHXParser();
5065 p3p.setIgnoreQuotes( false );
5066 final Phylogeny p3 = factory.create( "(\"A)\",'B1')", p3p )[ 0 ];
5067 if ( !p3.toNewHampshire().equals( "('A)',B1);" ) ) {
5070 final NHXParser p4p = new NHXParser();
5071 p4p.setIgnoreQuotes( false );
5072 final Phylogeny p4 = factory.create( "(\"A)\",'B(),; x')", p4p )[ 0 ];
5073 if ( !p4.toNewHampshire().equals( "('A)','B(),; x');" ) ) {
5076 final Phylogeny p10 = factory
5077 .create( " [79] ( (\"A \n\tB \" [co mment] :0 .2[comment],'B':0.3[com])[com ment]: 0. 5 \t[ 9 1 ][ comment],'C (or D?\\//;,))': 0.1)[comment]'\nroot is here (cool, was! ) ':0.1[100] [comment]",
5078 new NHXParser() )[ 0 ];
5079 final String p10_clean_str = "(('A B':0.2,B:0.3):0.5[&&NHX:B=91],'C (or D?\\//;,))':0.1)'root is here (cool, was! )':0.1[&&NHX:B=100]";
5080 if ( !p10.toNewHampshireX().equals( p10_clean_str ) ) {
5083 final Phylogeny p11 = factory.create( p10.toNewHampshireX(), new NHXParser() )[ 0 ];
5084 if ( !p11.toNewHampshireX().equals( p10_clean_str ) ) {
5088 final Phylogeny p12 = factory
5089 .create( " [79] ( (\"A \n\tB \" [[][] :0 .2[comment][\t&\t&\n N\tH\tX:S=mo\tnkey !],'\tB\t\b\t\n\f\rB B ':0.0\b3[])\t[com ment]: 0. 5 \t[ 9 1 ][ \ncomment],'C\t (or D?\\//;,))': 0.\b1)[comment]'\nroot \tis here (cool, \b\t\n\f\r was! ) ':0.1[100] [comment]",
5090 new NHXParser() )[ 0 ];
5091 final String p12_clean_str = "(('A B':0.2[&&NHX:S=monkey!],'BB B':0.03):0.5[&&NHX:B=91],'C (or D?\\//;,))':0.1)'root is here (cool, was! )':0.1[&&NHX:B=100]";
5092 if ( !p12.toNewHampshireX().equals( p12_clean_str ) ) {
5095 final Phylogeny p13 = factory.create( p12.toNewHampshireX(), new NHXParser() )[ 0 ];
5096 if ( !p13.toNewHampshireX().equals( p12_clean_str ) ) {
5099 final String p12_clean_str_nh = "(('A B':0.2,'BB B':0.03):0.5,'C (or D?\\//;,))':0.1)'root is here (cool, was! )':0.1;";
5100 if ( !p13.toNewHampshire().equals( p12_clean_str_nh ) ) {
5103 final Phylogeny p14 = factory.create( p13.toNewHampshire(), new NHXParser() )[ 0 ];
5104 if ( !p14.toNewHampshire().equals( p12_clean_str_nh ) ) {
5108 catch ( final Exception e ) {
5109 e.printStackTrace( System.out );
5115 private static boolean testNHXParsingMB() {
5117 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
5118 final Phylogeny p1 = factory.create( "(1[&prob=0.9500000000000000e+00,prob_stddev=0.1100000000000000e+00,"
5119 + "prob_range={1.000000000000000e+00,1.000000000000000e+00},prob(percent)=\"100\","
5120 + "prob+-sd=\"100+-0\"]:4.129000000000000e-02[&length_mean=4.153987461671767e-02,"
5121 + "length_median=4.129000000000000e-02,length_95%HPD={3.217800000000000e-02,"
5122 + "5.026800000000000e-02}],2[&prob=0.810000000000000e+00,prob_stddev=0.000000000000000e+00,"
5123 + "prob_range={1.000000000000000e+00,1.000000000000000e+00},prob(percent)=\"100\","
5124 + "prob+-sd=\"100+-0\"]:6.375699999999999e-02[&length_mean=6.395210411945065e-02,"
5125 + "length_median=6.375699999999999e-02,length_95%HPD={5.388600000000000e-02,"
5126 + "7.369400000000000e-02}])", new NHXParser() )[ 0 ];
5127 if ( !isEqual( p1.getNode( "1" ).getDistanceToParent(), 4.129e-02 ) ) {
5130 if ( !isEqual( p1.getNode( "1" ).getBranchData().getConfidence( 0 ).getValue(), 0.9500000000000000e+00 ) ) {
5133 if ( !isEqual( p1.getNode( "1" ).getBranchData().getConfidence( 0 ).getStandardDeviation(),
5134 0.1100000000000000e+00 ) ) {
5137 if ( !isEqual( p1.getNode( "2" ).getDistanceToParent(), 6.375699999999999e-02 ) ) {
5140 if ( !isEqual( p1.getNode( "2" ).getBranchData().getConfidence( 0 ).getValue(), 0.810000000000000e+00 ) ) {
5143 final Phylogeny p2 = factory
5144 .create( "(1[something_else(?)s,prob=0.9500000000000000e+00{}(((,p)rob_stddev=0.110000000000e+00,"
5145 + "prob_range={1.000000000000000e+00,1.000000000000000e+00},prob(percent)=\"100\","
5146 + "prob+-sd=\"100+-0\"]:4.129000000000000e-02[&length_mean=4.153987461671767e-02,"
5147 + "length_median=4.129000000000000e-02,length_95%HPD={3.217800000000000e-02,"
5148 + "5.026800000000000e-02}],2[&prob=0.810000000000000e+00,prob_stddev=0.000000000000000e+00,"
5149 + "prob_range={1.000000000000000e+00,1.000000000000000e+00},prob(percent)=\"100\","
5150 + "prob+-sd=\"100+-0\"]:6.375699999999999e-02[&length_mean=6.395210411945065e-02,"
5151 + "length_median=6.375699999999999e-02,length_95%HPD={5.388600000000000e-02,"
5152 + "7.369400000000000e-02}])",
5153 new NHXParser() )[ 0 ];
5154 if ( p2.getNode( "1" ) == null ) {
5157 if ( p2.getNode( "2" ) == null ) {
5161 catch ( final Exception e ) {
5162 e.printStackTrace( System.out );
5169 private static boolean testPhylogenyBranch() {
5171 final PhylogenyNode a1 = PhylogenyNode.createInstanceFromNhxString( "a" );
5172 final PhylogenyNode b1 = PhylogenyNode.createInstanceFromNhxString( "b" );
5173 final PhylogenyBranch a1b1 = new PhylogenyBranch( a1, b1 );
5174 final PhylogenyBranch b1a1 = new PhylogenyBranch( b1, a1 );
5175 if ( !a1b1.equals( a1b1 ) ) {
5178 if ( !a1b1.equals( b1a1 ) ) {
5181 if ( !b1a1.equals( a1b1 ) ) {
5184 final PhylogenyBranch a1_b1 = new PhylogenyBranch( a1, b1, true );
5185 final PhylogenyBranch b1_a1 = new PhylogenyBranch( b1, a1, true );
5186 final PhylogenyBranch a1_b1_ = new PhylogenyBranch( a1, b1, false );
5187 if ( a1_b1.equals( b1_a1 ) ) {
5190 if ( a1_b1.equals( a1_b1_ ) ) {
5193 final PhylogenyBranch b1_a1_ = new PhylogenyBranch( b1, a1, false );
5194 if ( !a1_b1.equals( b1_a1_ ) ) {
5197 if ( a1_b1_.equals( b1_a1_ ) ) {
5200 if ( !a1_b1_.equals( b1_a1 ) ) {
5204 catch ( final Exception e ) {
5205 e.printStackTrace( System.out );
5211 private static boolean testPhyloXMLparsingOfDistributionElement() {
5213 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
5214 PhyloXmlParser xml_parser = null;
5216 xml_parser = PhyloXmlParser.createPhyloXmlParserXsdValidating();
5218 catch ( final Exception e ) {
5219 // Do nothing -- means were not running from jar.
5221 if ( xml_parser == null ) {
5222 xml_parser = new PhyloXmlParser();
5223 if ( USE_LOCAL_PHYLOXML_SCHEMA ) {
5224 xml_parser.setValidateAgainstSchema( PHYLOXML_LOCAL_XSD );
5227 xml_parser.setValidateAgainstSchema( PHYLOXML_REMOTE_XSD );
5230 final Phylogeny[] phylogenies_0 = factory.create( Test.PATH_TO_TEST_DATA + "phyloxml_distribution.xml",
5232 if ( xml_parser.getErrorCount() > 0 ) {
5233 System.out.println( xml_parser.getErrorMessages().toString() );
5236 if ( phylogenies_0.length != 1 ) {
5239 final Phylogeny t1 = phylogenies_0[ 0 ];
5240 PhylogenyNode n = null;
5241 Distribution d = null;
5242 n = t1.getNode( "root node" );
5243 if ( !n.getNodeData().isHasDistribution() ) {
5246 if ( n.getNodeData().getDistributions().size() != 1 ) {
5249 d = n.getNodeData().getDistribution();
5250 if ( !d.getDesc().equals( "Hirschweg 38" ) ) {
5253 if ( d.getPoints().size() != 1 ) {
5256 if ( d.getPolygons() != null ) {
5259 if ( !d.getPoints().get( 0 ).getAltitude().toString().equals( "472" ) ) {
5262 if ( !d.getPoints().get( 0 ).getAltiudeUnit().equals( "m" ) ) {
5265 if ( !d.getPoints().get( 0 ).getGeodeticDatum().equals( "WGS84" ) ) {
5268 if ( !d.getPoints().get( 0 ).getLatitude().toString().equals( "47.48148427110029" ) ) {
5271 if ( !d.getPoints().get( 0 ).getLongitude().toString().equals( "8.768951296806335" ) ) {
5274 n = t1.getNode( "node a" );
5275 if ( !n.getNodeData().isHasDistribution() ) {
5278 if ( n.getNodeData().getDistributions().size() != 2 ) {
5281 d = n.getNodeData().getDistribution( 1 );
5282 if ( !d.getDesc().equals( "San Diego" ) ) {
5285 if ( d.getPoints().size() != 1 ) {
5288 if ( d.getPolygons() != null ) {
5291 if ( !d.getPoints().get( 0 ).getAltitude().toString().equals( "104" ) ) {
5294 if ( !d.getPoints().get( 0 ).getAltiudeUnit().equals( "m" ) ) {
5297 if ( !d.getPoints().get( 0 ).getGeodeticDatum().equals( "WGS84" ) ) {
5300 if ( !d.getPoints().get( 0 ).getLatitude().toString().equals( "32.880933" ) ) {
5303 if ( !d.getPoints().get( 0 ).getLongitude().toString().equals( "-117.217543" ) ) {
5306 n = t1.getNode( "node bb" );
5307 if ( !n.getNodeData().isHasDistribution() ) {
5310 if ( n.getNodeData().getDistributions().size() != 1 ) {
5313 d = n.getNodeData().getDistribution( 0 );
5314 if ( d.getPoints().size() != 3 ) {
5317 if ( d.getPolygons().size() != 2 ) {
5320 if ( !d.getPoints().get( 0 ).getLatitude().toString().equals( "1" ) ) {
5323 if ( !d.getPoints().get( 0 ).getLongitude().toString().equals( "2" ) ) {
5326 if ( !d.getPoints().get( 1 ).getLatitude().toString().equals( "3" ) ) {
5329 if ( !d.getPoints().get( 1 ).getLongitude().toString().equals( "4" ) ) {
5332 if ( !d.getPoints().get( 2 ).getLatitude().toString().equals( "5" ) ) {
5335 if ( !d.getPoints().get( 2 ).getLongitude().toString().equals( "6" ) ) {
5338 Polygon p = d.getPolygons().get( 0 );
5339 if ( p.getPoints().size() != 3 ) {
5342 if ( !p.getPoints().get( 0 ).getLatitude().toString().equals( "0.1" ) ) {
5345 if ( !p.getPoints().get( 0 ).getLongitude().toString().equals( "0.2" ) ) {
5348 if ( !p.getPoints().get( 0 ).getAltitude().toString().equals( "10" ) ) {
5351 if ( !p.getPoints().get( 2 ).getLatitude().toString().equals( "0.5" ) ) {
5354 if ( !p.getPoints().get( 2 ).getLongitude().toString().equals( "0.6" ) ) {
5357 if ( !p.getPoints().get( 2 ).getAltitude().toString().equals( "30" ) ) {
5360 p = d.getPolygons().get( 1 );
5361 if ( p.getPoints().size() != 3 ) {
5364 if ( !p.getPoints().get( 0 ).getLatitude().toString().equals( "1.49348902489947473" ) ) {
5367 if ( !p.getPoints().get( 0 ).getLongitude().toString().equals( "2.567489393947847492" ) ) {
5370 if ( !p.getPoints().get( 0 ).getAltitude().toString().equals( "10" ) ) {
5374 final StringBuffer t1_sb = new StringBuffer( t1.toPhyloXML( 0 ) );
5375 final Phylogeny[] rt = factory.create( t1_sb, xml_parser );
5376 if ( rt.length != 1 ) {
5379 final Phylogeny t1_rt = rt[ 0 ];
5380 n = t1_rt.getNode( "root node" );
5381 if ( !n.getNodeData().isHasDistribution() ) {
5384 if ( n.getNodeData().getDistributions().size() != 1 ) {
5387 d = n.getNodeData().getDistribution();
5388 if ( !d.getDesc().equals( "Hirschweg 38" ) ) {
5391 if ( d.getPoints().size() != 1 ) {
5394 if ( d.getPolygons() != null ) {
5397 if ( !d.getPoints().get( 0 ).getAltitude().toString().equals( "472" ) ) {
5400 if ( !d.getPoints().get( 0 ).getAltiudeUnit().equals( "m" ) ) {
5403 if ( !d.getPoints().get( 0 ).getGeodeticDatum().equals( "WGS84" ) ) {
5406 if ( !d.getPoints().get( 0 ).getLatitude().toString().equals( "47.48148427110029" ) ) {
5409 if ( !d.getPoints().get( 0 ).getLongitude().toString().equals( "8.768951296806335" ) ) {
5412 n = t1_rt.getNode( "node a" );
5413 if ( !n.getNodeData().isHasDistribution() ) {
5416 if ( n.getNodeData().getDistributions().size() != 2 ) {
5419 d = n.getNodeData().getDistribution( 1 );
5420 if ( !d.getDesc().equals( "San Diego" ) ) {
5423 if ( d.getPoints().size() != 1 ) {
5426 if ( d.getPolygons() != null ) {
5429 if ( !d.getPoints().get( 0 ).getAltitude().toString().equals( "104" ) ) {
5432 if ( !d.getPoints().get( 0 ).getAltiudeUnit().equals( "m" ) ) {
5435 if ( !d.getPoints().get( 0 ).getGeodeticDatum().equals( "WGS84" ) ) {
5438 if ( !d.getPoints().get( 0 ).getLatitude().toString().equals( "32.880933" ) ) {
5441 if ( !d.getPoints().get( 0 ).getLongitude().toString().equals( "-117.217543" ) ) {
5444 n = t1_rt.getNode( "node bb" );
5445 if ( !n.getNodeData().isHasDistribution() ) {
5448 if ( n.getNodeData().getDistributions().size() != 1 ) {
5451 d = n.getNodeData().getDistribution( 0 );
5452 if ( d.getPoints().size() != 3 ) {
5455 if ( d.getPolygons().size() != 2 ) {
5458 if ( !d.getPoints().get( 0 ).getLatitude().toString().equals( "1" ) ) {
5461 if ( !d.getPoints().get( 0 ).getLongitude().toString().equals( "2" ) ) {
5464 if ( !d.getPoints().get( 1 ).getLatitude().toString().equals( "3" ) ) {
5467 if ( !d.getPoints().get( 1 ).getLongitude().toString().equals( "4" ) ) {
5470 if ( !d.getPoints().get( 2 ).getLatitude().toString().equals( "5" ) ) {
5473 if ( !d.getPoints().get( 2 ).getLongitude().toString().equals( "6" ) ) {
5476 p = d.getPolygons().get( 0 );
5477 if ( p.getPoints().size() != 3 ) {
5480 if ( !p.getPoints().get( 0 ).getLatitude().toString().equals( "0.1" ) ) {
5483 if ( !p.getPoints().get( 0 ).getLongitude().toString().equals( "0.2" ) ) {
5486 if ( !p.getPoints().get( 0 ).getAltitude().toString().equals( "10" ) ) {
5489 if ( !p.getPoints().get( 2 ).getLatitude().toString().equals( "0.5" ) ) {
5492 if ( !p.getPoints().get( 2 ).getLongitude().toString().equals( "0.6" ) ) {
5495 if ( !p.getPoints().get( 2 ).getAltitude().toString().equals( "30" ) ) {
5498 p = d.getPolygons().get( 1 );
5499 if ( p.getPoints().size() != 3 ) {
5502 if ( !p.getPoints().get( 0 ).getLatitude().toString().equals( "1.49348902489947473" ) ) {
5505 if ( !p.getPoints().get( 0 ).getLongitude().toString().equals( "2.567489393947847492" ) ) {
5508 if ( !p.getPoints().get( 0 ).getAltitude().toString().equals( "10" ) ) {
5512 catch ( final Exception e ) {
5513 e.printStackTrace( System.out );
5519 private static boolean testPostOrderIterator() {
5521 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
5522 final Phylogeny t0 = factory.create( "((A,B)ab,(C,D)cd)r", new NHXParser() )[ 0 ];
5523 PhylogenyNodeIterator it0;
5524 for( it0 = t0.iteratorPostorder(); it0.hasNext(); ) {
5527 for( it0.reset(); it0.hasNext(); ) {
5530 final Phylogeny t1 = factory.create( "(((A,B)ab,(C,D)cd)abcd,((E,F)ef,(G,H)gh)efgh)r", new NHXParser() )[ 0 ];
5531 final PhylogenyNodeIterator it = t1.iteratorPostorder();
5532 if ( !it.next().getName().equals( "A" ) ) {
5535 if ( !it.next().getName().equals( "B" ) ) {
5538 if ( !it.next().getName().equals( "ab" ) ) {
5541 if ( !it.next().getName().equals( "C" ) ) {
5544 if ( !it.next().getName().equals( "D" ) ) {
5547 if ( !it.next().getName().equals( "cd" ) ) {
5550 if ( !it.next().getName().equals( "abcd" ) ) {
5553 if ( !it.next().getName().equals( "E" ) ) {
5556 if ( !it.next().getName().equals( "F" ) ) {
5559 if ( !it.next().getName().equals( "ef" ) ) {
5562 if ( !it.next().getName().equals( "G" ) ) {
5565 if ( !it.next().getName().equals( "H" ) ) {
5568 if ( !it.next().getName().equals( "gh" ) ) {
5571 if ( !it.next().getName().equals( "efgh" ) ) {
5574 if ( !it.next().getName().equals( "r" ) ) {
5577 if ( it.hasNext() ) {
5581 catch ( final Exception e ) {
5582 e.printStackTrace( System.out );
5588 private static boolean testPreOrderIterator() {
5590 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
5591 final Phylogeny t0 = factory.create( "((A,B)ab,(C,D)cd)r", new NHXParser() )[ 0 ];
5592 PhylogenyNodeIterator it0;
5593 for( it0 = t0.iteratorPreorder(); it0.hasNext(); ) {
5596 for( it0.reset(); it0.hasNext(); ) {
5599 PhylogenyNodeIterator it = t0.iteratorPreorder();
5600 if ( !it.next().getName().equals( "r" ) ) {
5603 if ( !it.next().getName().equals( "ab" ) ) {
5606 if ( !it.next().getName().equals( "A" ) ) {
5609 if ( !it.next().getName().equals( "B" ) ) {
5612 if ( !it.next().getName().equals( "cd" ) ) {
5615 if ( !it.next().getName().equals( "C" ) ) {
5618 if ( !it.next().getName().equals( "D" ) ) {
5621 if ( it.hasNext() ) {
5624 final Phylogeny t1 = factory.create( "(((A,B)ab,(C,D)cd)abcd,((E,F)ef,(G,H)gh)efgh)r", new NHXParser() )[ 0 ];
5625 it = t1.iteratorPreorder();
5626 if ( !it.next().getName().equals( "r" ) ) {
5629 if ( !it.next().getName().equals( "abcd" ) ) {
5632 if ( !it.next().getName().equals( "ab" ) ) {
5635 if ( !it.next().getName().equals( "A" ) ) {
5638 if ( !it.next().getName().equals( "B" ) ) {
5641 if ( !it.next().getName().equals( "cd" ) ) {
5644 if ( !it.next().getName().equals( "C" ) ) {
5647 if ( !it.next().getName().equals( "D" ) ) {
5650 if ( !it.next().getName().equals( "efgh" ) ) {
5653 if ( !it.next().getName().equals( "ef" ) ) {
5656 if ( !it.next().getName().equals( "E" ) ) {
5659 if ( !it.next().getName().equals( "F" ) ) {
5662 if ( !it.next().getName().equals( "gh" ) ) {
5665 if ( !it.next().getName().equals( "G" ) ) {
5668 if ( !it.next().getName().equals( "H" ) ) {
5671 if ( it.hasNext() ) {
5675 catch ( final Exception e ) {
5676 e.printStackTrace( System.out );
5682 private static boolean testPropertiesMap() {
5684 final PropertiesMap pm = new PropertiesMap();
5685 final Property p0 = new Property( "dimensions:diameter", "1", "metric:mm", "xsd:decimal", AppliesTo.NODE );
5686 final Property p1 = new Property( "dimensions:length", "2", "metric:mm", "xsd:decimal", AppliesTo.NODE );
5687 final Property p2 = new Property( "something:else",
5689 "improbable:research",
5692 pm.addProperty( p0 );
5693 pm.addProperty( p1 );
5694 pm.addProperty( p2 );
5695 if ( !pm.getProperty( "dimensions:diameter" ).getValue().equals( "1" ) ) {
5698 if ( !pm.getProperty( "dimensions:length" ).getValue().equals( "2" ) ) {
5701 if ( pm.getProperties().size() != 3 ) {
5704 if ( pm.getPropertiesWithGivenReferencePrefix( "dimensions" ).size() != 2 ) {
5707 if ( pm.getPropertiesWithGivenReferencePrefix( "something" ).size() != 1 ) {
5710 if ( pm.getProperties().size() != 3 ) {
5713 pm.removeProperty( "dimensions:diameter" );
5714 if ( pm.getProperties().size() != 2 ) {
5717 if ( pm.getPropertiesWithGivenReferencePrefix( "dimensions" ).size() != 1 ) {
5720 if ( pm.getPropertiesWithGivenReferencePrefix( "something" ).size() != 1 ) {
5724 catch ( final Exception e ) {
5725 e.printStackTrace( System.out );
5731 private static boolean testReIdMethods() {
5733 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
5734 final Phylogeny p = factory.create( "((1,2)A,(((X,Y,Z)a,b)3)B,(4,5,6)C)r", new NHXParser() )[ 0 ];
5735 final int count = PhylogenyNode.getNodeCount();
5737 if ( p.getNode( "r" ).getId() != count ) {
5740 if ( p.getNode( "A" ).getId() != count + 1 ) {
5743 if ( p.getNode( "B" ).getId() != count + 1 ) {
5746 if ( p.getNode( "C" ).getId() != count + 1 ) {
5749 if ( p.getNode( "1" ).getId() != count + 2 ) {
5752 if ( p.getNode( "2" ).getId() != count + 2 ) {
5755 if ( p.getNode( "3" ).getId() != count + 2 ) {
5758 if ( p.getNode( "4" ).getId() != count + 2 ) {
5761 if ( p.getNode( "5" ).getId() != count + 2 ) {
5764 if ( p.getNode( "6" ).getId() != count + 2 ) {
5767 if ( p.getNode( "a" ).getId() != count + 3 ) {
5770 if ( p.getNode( "b" ).getId() != count + 3 ) {
5773 if ( p.getNode( "X" ).getId() != count + 4 ) {
5776 if ( p.getNode( "Y" ).getId() != count + 4 ) {
5779 if ( p.getNode( "Z" ).getId() != count + 4 ) {
5783 catch ( final Exception e ) {
5784 e.printStackTrace( System.out );
5790 private static boolean testRerooting() {
5792 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
5793 final Phylogeny t1 = factory.create( "((A:1,B:2)AB:1[&&NHX:B=55],(C:3,D:5)CD:3[&&NHX:B=10])ABCD:0.5",
5794 new NHXParser() )[ 0 ];
5795 if ( !t1.isRooted() ) {
5798 t1.reRoot( t1.getNode( "D" ) );
5799 t1.reRoot( t1.getNode( "CD" ) );
5800 t1.reRoot( t1.getNode( "A" ) );
5801 t1.reRoot( t1.getNode( "B" ) );
5802 t1.reRoot( t1.getNode( "AB" ) );
5803 t1.reRoot( t1.getNode( "D" ) );
5804 t1.reRoot( t1.getNode( "C" ) );
5805 t1.reRoot( t1.getNode( "CD" ) );
5806 t1.reRoot( t1.getNode( "A" ) );
5807 t1.reRoot( t1.getNode( "B" ) );
5808 t1.reRoot( t1.getNode( "AB" ) );
5809 t1.reRoot( t1.getNode( "D" ) );
5810 t1.reRoot( t1.getNode( "D" ) );
5811 t1.reRoot( t1.getNode( "C" ) );
5812 t1.reRoot( t1.getNode( "A" ) );
5813 t1.reRoot( t1.getNode( "B" ) );
5814 t1.reRoot( t1.getNode( "AB" ) );
5815 t1.reRoot( t1.getNode( "C" ) );
5816 t1.reRoot( t1.getNode( "D" ) );
5817 t1.reRoot( t1.getNode( "CD" ) );
5818 t1.reRoot( t1.getNode( "D" ) );
5819 t1.reRoot( t1.getNode( "A" ) );
5820 t1.reRoot( t1.getNode( "B" ) );
5821 t1.reRoot( t1.getNode( "AB" ) );
5822 t1.reRoot( t1.getNode( "C" ) );
5823 t1.reRoot( t1.getNode( "D" ) );
5824 t1.reRoot( t1.getNode( "CD" ) );
5825 t1.reRoot( t1.getNode( "D" ) );
5826 if ( !isEqual( t1.getNode( "A" ).getDistanceToParent(), 1 ) ) {
5829 if ( !isEqual( t1.getNode( "B" ).getDistanceToParent(), 2 ) ) {
5832 if ( !isEqual( t1.getNode( "C" ).getDistanceToParent(), 3 ) ) {
5835 if ( !isEqual( t1.getNode( "D" ).getDistanceToParent(), 2.5 ) ) {
5838 if ( !isEqual( t1.getNode( "CD" ).getDistanceToParent(), 2.5 ) ) {
5841 if ( !isEqual( t1.getNode( "AB" ).getDistanceToParent(), 4 ) ) {
5844 final Phylogeny t2 = factory.create( "(((A:1,B:2)AB:10[&&NHX:B=55],C)ABC:3[&&NHX:B=33],D:5)ABCD:0.5",
5845 new NHXParser() )[ 0 ];
5846 t2.reRoot( t2.getNode( "A" ) );
5847 t2.reRoot( t2.getNode( "D" ) );
5848 t2.reRoot( t2.getNode( "ABC" ) );
5849 t2.reRoot( t2.getNode( "A" ) );
5850 t2.reRoot( t2.getNode( "B" ) );
5851 t2.reRoot( t2.getNode( "D" ) );
5852 t2.reRoot( t2.getNode( "C" ) );
5853 t2.reRoot( t2.getNode( "ABC" ) );
5854 t2.reRoot( t2.getNode( "A" ) );
5855 t2.reRoot( t2.getNode( "B" ) );
5856 t2.reRoot( t2.getNode( "AB" ) );
5857 t2.reRoot( t2.getNode( "AB" ) );
5858 t2.reRoot( t2.getNode( "D" ) );
5859 t2.reRoot( t2.getNode( "C" ) );
5860 t2.reRoot( t2.getNode( "B" ) );
5861 t2.reRoot( t2.getNode( "AB" ) );
5862 t2.reRoot( t2.getNode( "D" ) );
5863 t2.reRoot( t2.getNode( "D" ) );
5864 t2.reRoot( t2.getNode( "ABC" ) );
5865 t2.reRoot( t2.getNode( "A" ) );
5866 t2.reRoot( t2.getNode( "B" ) );
5867 t2.reRoot( t2.getNode( "AB" ) );
5868 t2.reRoot( t2.getNode( "D" ) );
5869 t2.reRoot( t2.getNode( "C" ) );
5870 t2.reRoot( t2.getNode( "ABC" ) );
5871 t2.reRoot( t2.getNode( "A" ) );
5872 t2.reRoot( t2.getNode( "B" ) );
5873 t2.reRoot( t2.getNode( "AB" ) );
5874 t2.reRoot( t2.getNode( "D" ) );
5875 t2.reRoot( t2.getNode( "D" ) );
5876 t2.reRoot( t2.getNode( "C" ) );
5877 t2.reRoot( t2.getNode( "A" ) );
5878 t2.reRoot( t2.getNode( "B" ) );
5879 t2.reRoot( t2.getNode( "AB" ) );
5880 t2.reRoot( t2.getNode( "C" ) );
5881 t2.reRoot( t2.getNode( "D" ) );
5882 t2.reRoot( t2.getNode( "ABC" ) );
5883 t2.reRoot( t2.getNode( "D" ) );
5884 t2.reRoot( t2.getNode( "A" ) );
5885 t2.reRoot( t2.getNode( "B" ) );
5886 t2.reRoot( t2.getNode( "AB" ) );
5887 t2.reRoot( t2.getNode( "C" ) );
5888 t2.reRoot( t2.getNode( "D" ) );
5889 t2.reRoot( t2.getNode( "ABC" ) );
5890 t2.reRoot( t2.getNode( "D" ) );
5891 if ( !isEqual( t2.getNode( "AB" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
5894 if ( !isEqual( t2.getNode( "ABC" ).getBranchData().getConfidence( 0 ).getValue(), 33 ) ) {
5897 t2.reRoot( t2.getNode( "ABC" ) );
5898 if ( !isEqual( t2.getNode( "AB" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
5901 if ( !isEqual( t2.getNode( "ABC" ).getBranchData().getConfidence( 0 ).getValue(), 33 ) ) {
5904 t2.reRoot( t2.getNode( "AB" ) );
5905 if ( !isEqual( t2.getNode( "AB" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
5908 if ( !isEqual( t2.getNode( "ABC" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
5911 if ( !isEqual( t2.getNode( "D" ).getBranchData().getConfidence( 0 ).getValue(), 33 ) ) {
5914 t2.reRoot( t2.getNode( "AB" ) );
5915 if ( !isEqual( t2.getNode( "AB" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
5918 if ( !isEqual( t2.getNode( "ABC" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
5921 if ( !isEqual( t2.getNode( "D" ).getBranchData().getConfidence( 0 ).getValue(), 33 ) ) {
5924 t2.reRoot( t2.getNode( "D" ) );
5925 if ( !isEqual( t2.getNode( "AB" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
5928 if ( !isEqual( t2.getNode( "ABC" ).getBranchData().getConfidence( 0 ).getValue(), 33 ) ) {
5931 t2.reRoot( t2.getNode( "ABC" ) );
5932 if ( !isEqual( t2.getNode( "AB" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
5935 if ( !isEqual( t2.getNode( "ABC" ).getBranchData().getConfidence( 0 ).getValue(), 33 ) ) {
5938 final Phylogeny t3 = factory.create( "(A[&&NHX:B=10],B[&&NHX:B=20],C[&&NHX:B=30],D[&&NHX:B=40])",
5939 new NHXParser() )[ 0 ];
5940 t3.reRoot( t3.getNode( "B" ) );
5941 if ( t3.getNode( "B" ).getBranchData().getConfidence( 0 ).getValue() != 20 ) {
5944 if ( t3.getNode( "A" ).getParent().getBranchData().getConfidence( 0 ).getValue() != 20 ) {
5947 if ( t3.getNode( "A" ).getParent().getNumberOfDescendants() != 3 ) {
5950 t3.reRoot( t3.getNode( "B" ) );
5951 if ( t3.getNode( "B" ).getBranchData().getConfidence( 0 ).getValue() != 20 ) {
5954 if ( t3.getNode( "A" ).getParent().getBranchData().getConfidence( 0 ).getValue() != 20 ) {
5957 if ( t3.getNode( "A" ).getParent().getNumberOfDescendants() != 3 ) {
5960 t3.reRoot( t3.getRoot() );
5961 if ( t3.getNode( "B" ).getBranchData().getConfidence( 0 ).getValue() != 20 ) {
5964 if ( t3.getNode( "A" ).getParent().getBranchData().getConfidence( 0 ).getValue() != 20 ) {
5967 if ( t3.getNode( "A" ).getParent().getNumberOfDescendants() != 3 ) {
5971 catch ( final Exception e ) {
5972 e.printStackTrace( System.out );
5978 private static boolean testSDIse() {
5980 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
5981 final Phylogeny species1 = factory.create( "[&&NHX:S=yeast]", new NHXParser() )[ 0 ];
5982 final Phylogeny gene1 = factory.create( "(A1[&&NHX:S=yeast],A2[&&NHX:S=yeast])", new NHXParser() )[ 0 ];
5983 gene1.setRooted( true );
5984 species1.setRooted( true );
5985 final SDI sdi = new SDIse( gene1, species1 );
5986 if ( !gene1.getRoot().isDuplication() ) {
5989 final Phylogeny species2 = factory
5990 .create( "(((([&&NHX:S=A],[&&NHX:S=B]),[&&NHX:S=C]),[&&NHX:S=D]),([&&NHX:S=E],[&&NHX:S=F]))",
5991 new NHXParser() )[ 0 ];
5992 final Phylogeny gene2 = factory
5993 .create( "(((([&&NHX:S=A],[&&NHX:S=B])ab,[&&NHX:S=C])abc,[&&NHX:S=D])abcd,([&&NHX:S=E],[&&NHX:S=F])ef)r",
5994 new NHXParser() )[ 0 ];
5995 species2.setRooted( true );
5996 gene2.setRooted( true );
5997 final SDI sdi2 = new SDIse( gene2, species2 );
5998 if ( sdi2.getDuplicationsSum() != 0 ) {
6001 if ( !gene2.getNode( "ab" ).isSpeciation() ) {
6004 if ( !gene2.getNode( "ab" ).isHasAssignedEvent() ) {
6007 if ( !gene2.getNode( "abc" ).isSpeciation() ) {
6010 if ( !gene2.getNode( "abc" ).isHasAssignedEvent() ) {
6013 if ( !gene2.getNode( "r" ).isSpeciation() ) {
6016 if ( !gene2.getNode( "r" ).isHasAssignedEvent() ) {
6019 final Phylogeny species3 = factory
6020 .create( "(((([&&NHX:S=A],[&&NHX:S=B]),[&&NHX:S=C]),[&&NHX:S=D]),([&&NHX:S=E],[&&NHX:S=F]))",
6021 new NHXParser() )[ 0 ];
6022 final Phylogeny gene3 = factory
6023 .create( "(((([&&NHX:S=A],[&&NHX:S=A])aa,[&&NHX:S=C])abc,[&&NHX:S=D])abcd,([&&NHX:S=E],[&&NHX:S=F])ef)r",
6024 new NHXParser() )[ 0 ];
6025 species3.setRooted( true );
6026 gene3.setRooted( true );
6027 final SDI sdi3 = new SDIse( gene3, species3 );
6028 if ( sdi3.getDuplicationsSum() != 1 ) {
6031 if ( !gene3.getNode( "aa" ).isDuplication() ) {
6034 if ( !gene3.getNode( "aa" ).isHasAssignedEvent() ) {
6037 final Phylogeny species4 = factory
6038 .create( "(((([&&NHX:S=A],[&&NHX:S=B]),[&&NHX:S=C]),[&&NHX:S=D]),([&&NHX:S=E],[&&NHX:S=F]))",
6039 new NHXParser() )[ 0 ];
6040 final Phylogeny gene4 = factory
6041 .create( "(((([&&NHX:S=A],[&&NHX:S=C])ac,[&&NHX:S=B])abc,[&&NHX:S=D])abcd,([&&NHX:S=E],[&&NHX:S=F])ef)r",
6042 new NHXParser() )[ 0 ];
6043 species4.setRooted( true );
6044 gene4.setRooted( true );
6045 final SDI sdi4 = new SDIse( gene4, species4 );
6046 if ( sdi4.getDuplicationsSum() != 1 ) {
6049 if ( !gene4.getNode( "ac" ).isSpeciation() ) {
6052 if ( !gene4.getNode( "abc" ).isDuplication() ) {
6055 if ( gene4.getNode( "abcd" ).isDuplication() ) {
6058 if ( species4.getNumberOfExternalNodes() != 6 ) {
6061 if ( gene4.getNumberOfExternalNodes() != 6 ) {
6064 final Phylogeny species5 = factory
6065 .create( "(((([&&NHX:S=A],[&&NHX:S=B]),[&&NHX:S=C]),[&&NHX:S=D]),([&&NHX:S=E],[&&NHX:S=F]))",
6066 new NHXParser() )[ 0 ];
6067 final Phylogeny gene5 = factory
6068 .create( "(((([&&NHX:S=A],[&&NHX:S=D])ad,[&&NHX:S=C])adc,[&&NHX:S=B])abcd,([&&NHX:S=E],[&&NHX:S=F])ef)r",
6069 new NHXParser() )[ 0 ];
6070 species5.setRooted( true );
6071 gene5.setRooted( true );
6072 final SDI sdi5 = new SDIse( gene5, species5 );
6073 if ( sdi5.getDuplicationsSum() != 2 ) {
6076 if ( !gene5.getNode( "ad" ).isSpeciation() ) {
6079 if ( !gene5.getNode( "adc" ).isDuplication() ) {
6082 if ( !gene5.getNode( "abcd" ).isDuplication() ) {
6085 if ( species5.getNumberOfExternalNodes() != 6 ) {
6088 if ( gene5.getNumberOfExternalNodes() != 6 ) {
6091 // Trees from Louxin Zhang 1997 "On a Mirkin-Muchnik-Smith
6092 // Conjecture for Comparing Molecular Phylogenies"
6093 // J. of Comput Bio. Vol. 4, No 2, pp.177-187
6094 final Phylogeny species6 = factory
6095 .create( "(((1:[&&NHX:S=1],5:[&&NHX:S=5])1-5,((4:[&&NHX:S=4],6:[&&NHX:S=6])4-6,2:[&&NHX:S=2])4-6-2)1-5-4-6-2,"
6096 + "((9:[&&NHX:S=9],3:[&&NHX:S=3])9-3,(8:[&&NHX:S=8],7:[&&NHX:S=7])8-7)9-3-8-7)",
6097 new NHXParser() )[ 0 ];
6098 final Phylogeny gene6 = factory
6099 .create( "(((1:0.1[&&NHX:S=1],2:0.1[&&NHX:S=2])1-2:0.1,3:0.1[&&NHX:S=3])1-2-3:0.1,"
6100 + "((4:0.1[&&NHX:S=4],(5:0.1[&&NHX:S=5],6:0.1[&&NHX:S=6])5-6:0.1)4-5-6:0.1,"
6101 + "(7:0.1[&&NHX:S=7],(8:0.1[&&NHX:S=8],9:0.1[&&NHX:S=9])8-9:0.1)7-8-9:0.1)4-5-6-7-8-9:0.1)r;",
6102 new NHXParser() )[ 0 ];
6103 species6.setRooted( true );
6104 gene6.setRooted( true );
6105 final SDI sdi6 = new SDIse( gene6, species6 );
6106 if ( sdi6.getDuplicationsSum() != 3 ) {
6109 if ( !gene6.getNode( "r" ).isDuplication() ) {
6112 if ( !gene6.getNode( "4-5-6" ).isDuplication() ) {
6115 if ( !gene6.getNode( "7-8-9" ).isDuplication() ) {
6118 if ( !gene6.getNode( "1-2" ).isSpeciation() ) {
6121 if ( !gene6.getNode( "1-2-3" ).isSpeciation() ) {
6124 if ( !gene6.getNode( "5-6" ).isSpeciation() ) {
6127 if ( !gene6.getNode( "8-9" ).isSpeciation() ) {
6130 if ( !gene6.getNode( "4-5-6-7-8-9" ).isSpeciation() ) {
6133 sdi6.computeMappingCostL();
6134 if ( sdi6.computeMappingCostL() != 17 ) {
6137 if ( species6.getNumberOfExternalNodes() != 9 ) {
6140 if ( gene6.getNumberOfExternalNodes() != 9 ) {
6143 final Phylogeny species7 = Test.createPhylogeny( "(((((((" + "([&&NHX:S=a1],[&&NHX:S=a2]),"
6144 + "([&&NHX:S=b1],[&&NHX:S=b2])" + "),[&&NHX:S=x]),(" + "([&&NHX:S=m1],[&&NHX:S=m2]),"
6145 + "([&&NHX:S=n1],[&&NHX:S=n2])" + ")),(" + "([&&NHX:S=i1],[&&NHX:S=i2]),"
6146 + "([&&NHX:S=j1],[&&NHX:S=j2])" + ")),(" + "([&&NHX:S=e1],[&&NHX:S=e2]),"
6147 + "([&&NHX:S=f1],[&&NHX:S=f2])" + ")),[&&NHX:S=y]),[&&NHX:S=z])" );
6148 species7.setRooted( true );
6149 final Phylogeny gene7_1 = Test
6150 .createPhylogeny( "((((((((a1[&&NHX:S=a1],a2[&&NHX:S=a2]),b1[&&NHX:S=b1]),x[&&NHX:S=x]),m1[&&NHX:S=m1]),i1[&&NHX:S=i1]),e1[&&NHX:S=e1]),y[&&NHX:S=y]),z[&&NHX:S=z])" );
6151 gene7_1.setRooted( true );
6152 final SDI sdi7 = new SDIse( gene7_1, species7 );
6153 if ( sdi7.getDuplicationsSum() != 0 ) {
6156 if ( !Test.getEvent( gene7_1, "a1", "a2" ).isSpeciation() ) {
6159 if ( !Test.getEvent( gene7_1, "a1", "b1" ).isSpeciation() ) {
6162 if ( !Test.getEvent( gene7_1, "a1", "x" ).isSpeciation() ) {
6165 if ( !Test.getEvent( gene7_1, "a1", "m1" ).isSpeciation() ) {
6168 if ( !Test.getEvent( gene7_1, "a1", "i1" ).isSpeciation() ) {
6171 if ( !Test.getEvent( gene7_1, "a1", "e1" ).isSpeciation() ) {
6174 if ( !Test.getEvent( gene7_1, "a1", "y" ).isSpeciation() ) {
6177 if ( !Test.getEvent( gene7_1, "a1", "z" ).isSpeciation() ) {
6180 final Phylogeny gene7_2 = Test
6181 .createPhylogeny( "(((((((((a1[&&NHX:S=a1],a2[&&NHX:S=a2]),b1[&&NHX:S=b1]),x[&&NHX:S=x]),m1[&&NHX:S=m1]),i1[&&NHX:S=i1]),j2[&&NHX:S=j2]),e1[&&NHX:S=e1]),y[&&NHX:S=y]),z[&&NHX:S=z])" );
6182 gene7_2.setRooted( true );
6183 final SDI sdi7_2 = new SDIse( gene7_2, species7 );
6184 if ( sdi7_2.getDuplicationsSum() != 1 ) {
6187 if ( !Test.getEvent( gene7_2, "a1", "a2" ).isSpeciation() ) {
6190 if ( !Test.getEvent( gene7_2, "a1", "b1" ).isSpeciation() ) {
6193 if ( !Test.getEvent( gene7_2, "a1", "x" ).isSpeciation() ) {
6196 if ( !Test.getEvent( gene7_2, "a1", "m1" ).isSpeciation() ) {
6199 if ( !Test.getEvent( gene7_2, "a1", "i1" ).isSpeciation() ) {
6202 if ( !Test.getEvent( gene7_2, "a1", "j2" ).isDuplication() ) {
6205 if ( !Test.getEvent( gene7_2, "a1", "e1" ).isSpeciation() ) {
6208 if ( !Test.getEvent( gene7_2, "a1", "y" ).isSpeciation() ) {
6211 if ( !Test.getEvent( gene7_2, "a1", "z" ).isSpeciation() ) {
6215 catch ( final Exception e ) {
6221 private static boolean testSDIunrooted() {
6223 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
6224 final Phylogeny p0 = factory.create( "((((A,B)ab,(C1,C2)cc)abc,D)abcd,(E,F)ef)abcdef", new NHXParser() )[ 0 ];
6225 final List<PhylogenyBranch> l = SDIR.getBranchesInPreorder( p0 );
6226 final Iterator<PhylogenyBranch> iter = l.iterator();
6227 PhylogenyBranch br = iter.next();
6228 if ( !br.getFirstNode().getName().equals( "abcd" ) && !br.getFirstNode().getName().equals( "ef" ) ) {
6231 if ( !br.getSecondNode().getName().equals( "abcd" ) && !br.getSecondNode().getName().equals( "ef" ) ) {
6235 if ( !br.getFirstNode().getName().equals( "abcd" ) && !br.getFirstNode().getName().equals( "abc" ) ) {
6238 if ( !br.getSecondNode().getName().equals( "abcd" ) && !br.getSecondNode().getName().equals( "abc" ) ) {
6242 if ( !br.getFirstNode().getName().equals( "abc" ) && !br.getFirstNode().getName().equals( "ab" ) ) {
6245 if ( !br.getSecondNode().getName().equals( "abc" ) && !br.getSecondNode().getName().equals( "ab" ) ) {
6249 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "A" ) ) {
6252 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "A" ) ) {
6256 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "B" ) ) {
6259 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "B" ) ) {
6263 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "abc" ) ) {
6266 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "abc" ) ) {
6270 if ( !br.getFirstNode().getName().equals( "abc" ) && !br.getFirstNode().getName().equals( "cc" ) ) {
6273 if ( !br.getSecondNode().getName().equals( "abc" ) && !br.getSecondNode().getName().equals( "cc" ) ) {
6277 if ( !br.getFirstNode().getName().equals( "C1" ) && !br.getFirstNode().getName().equals( "cc" ) ) {
6280 if ( !br.getSecondNode().getName().equals( "C1" ) && !br.getSecondNode().getName().equals( "cc" ) ) {
6284 if ( !br.getFirstNode().getName().equals( "C2" ) && !br.getFirstNode().getName().equals( "cc" ) ) {
6287 if ( !br.getSecondNode().getName().equals( "C2" ) && !br.getSecondNode().getName().equals( "cc" ) ) {
6291 if ( !br.getFirstNode().getName().equals( "abc" ) && !br.getFirstNode().getName().equals( "cc" ) ) {
6294 if ( !br.getSecondNode().getName().equals( "abc" ) && !br.getSecondNode().getName().equals( "cc" ) ) {
6298 if ( !br.getFirstNode().getName().equals( "abc" ) && !br.getFirstNode().getName().equals( "abcd" ) ) {
6301 if ( !br.getSecondNode().getName().equals( "abc" ) && !br.getSecondNode().getName().equals( "abcd" ) ) {
6305 if ( !br.getFirstNode().getName().equals( "abcd" ) && !br.getFirstNode().getName().equals( "D" ) ) {
6308 if ( !br.getSecondNode().getName().equals( "abcd" ) && !br.getSecondNode().getName().equals( "D" ) ) {
6312 if ( !br.getFirstNode().getName().equals( "ef" ) && !br.getFirstNode().getName().equals( "abcd" ) ) {
6315 if ( !br.getSecondNode().getName().equals( "ef" ) && !br.getSecondNode().getName().equals( "abcd" ) ) {
6319 if ( !br.getFirstNode().getName().equals( "ef" ) && !br.getFirstNode().getName().equals( "E" ) ) {
6322 if ( !br.getSecondNode().getName().equals( "ef" ) && !br.getSecondNode().getName().equals( "E" ) ) {
6326 if ( !br.getFirstNode().getName().equals( "ef" ) && !br.getFirstNode().getName().equals( "F" ) ) {
6329 if ( !br.getSecondNode().getName().equals( "ef" ) && !br.getSecondNode().getName().equals( "F" ) ) {
6332 if ( iter.hasNext() ) {
6335 final Phylogeny p1 = factory.create( "(C,(A,B)ab)abc", new NHXParser() )[ 0 ];
6336 final List<PhylogenyBranch> l1 = SDIR.getBranchesInPreorder( p1 );
6337 final Iterator<PhylogenyBranch> iter1 = l1.iterator();
6339 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "C" ) ) {
6342 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "C" ) ) {
6346 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "A" ) ) {
6349 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "A" ) ) {
6353 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "B" ) ) {
6356 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "B" ) ) {
6359 if ( iter1.hasNext() ) {
6362 final Phylogeny p2 = factory.create( "((A,B)ab,C)abc", new NHXParser() )[ 0 ];
6363 final List<PhylogenyBranch> l2 = SDIR.getBranchesInPreorder( p2 );
6364 final Iterator<PhylogenyBranch> iter2 = l2.iterator();
6366 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "C" ) ) {
6369 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "C" ) ) {
6373 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "A" ) ) {
6376 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "A" ) ) {
6380 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "B" ) ) {
6383 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "B" ) ) {
6386 if ( iter2.hasNext() ) {
6389 final Phylogeny species0 = factory
6390 .create( "(((([&&NHX:S=A],[&&NHX:S=B]),[&&NHX:S=C]),[&&NHX:S=D]),([&&NHX:S=E],[&&NHX:S=F]))",
6391 new NHXParser() )[ 0 ];
6392 final Phylogeny gene1 = factory
6393 .create( "(((((A:0.6[&&NHX:S=A],B:0.1[&&NHX:S=B])ab:0.1,C:0.1[&&NHX:S=C])abc:0.3,D:1.0[&&NHX:S=D])abcd:0.2,E:0.1[&&NHX:S=E])abcde:0.2,F:0.2[&&NHX:S=F])",
6394 new NHXParser() )[ 0 ];
6395 species0.setRooted( true );
6396 gene1.setRooted( true );
6397 final SDIR sdi_unrooted = new SDIR();
6398 sdi_unrooted.infer( gene1, species0, false, true, true, true, 10 );
6399 if ( sdi_unrooted.getCount() != 1 ) {
6402 if ( sdi_unrooted.getMinimalDuplications() != 0 ) {
6405 if ( !Test.isEqual( sdi_unrooted.getMinimalDiffInSubTreeHeights(), 0.4 ) ) {
6408 if ( !Test.isEqual( sdi_unrooted.getMinimalTreeHeight(), 1.0 ) ) {
6411 if ( sdi_unrooted.getMinimalMappingCost() != Integer.MAX_VALUE ) {
6414 final Phylogeny gene2 = factory
6415 .create( "(((((A:2.6[&&NHX:S=A],B:0.1[&&NHX:S=B])ab:0.1,C:0.1[&&NHX:S=C])abc:0.3,D:1.0[&&NHX:S=D])abcd:0.2,E:0.1[&&NHX:S=E])abcde:0.2,F:0.2[&&NHX:S=F])",
6416 new NHXParser() )[ 0 ];
6417 gene2.setRooted( true );
6418 sdi_unrooted.infer( gene2, species0, false, false, true, true, 10 );
6419 if ( sdi_unrooted.getCount() != 1 ) {
6422 if ( sdi_unrooted.getMinimalDuplications() != 3 ) {
6425 if ( !Test.isEqual( sdi_unrooted.getMinimalDiffInSubTreeHeights(), 0.0 ) ) {
6428 if ( !Test.isEqual( sdi_unrooted.getMinimalTreeHeight(), 2.0 ) ) {
6431 if ( sdi_unrooted.getMinimalMappingCost() != Integer.MAX_VALUE ) {
6434 final Phylogeny species6 = factory
6435 .create( "(((1:[&&NHX:S=1],5:[&&NHX:S=5])1-5,((4:[&&NHX:S=4],6:[&&NHX:S=6])4-6,2:[&&NHX:S=2])4-6-2)1-5-4-6-2,"
6436 + "((9:[&&NHX:S=9],3:[&&NHX:S=3])9-3,(8:[&&NHX:S=8],7:[&&NHX:S=7])8-7)9-3-8-7)",
6437 new NHXParser() )[ 0 ];
6438 final Phylogeny gene6 = factory
6439 .create( "((5:0.1[&&NHX:S=5],6:0.1[&&NHX:S=6])5-6:0.05[&&NHX:S=6],(4:0.1[&&NHX:S=4],"
6440 + "(((1:0.1[&&NHX:S=1],2:0.1[&&NHX:S=2])1-2:0.1[&&NHX:S=2],3:0.25[&&NHX:S=3])1-2-3:0.2[&&NHX:S=2],"
6441 + "(7:0.1[&&NHX:S=7],(8:0.1[&&NHX:S=8],"
6442 + "9:0.1[&&NHX:S=9])8-9:0.1[&&NHX:S=9])7-8-9:0.1[&&NHX:S=8])"
6443 + "4-5-6-7-8-9:0.1[&&NHX:S=5])4-5-6:0.05[&&NHX:S=5])",
6444 new NHXParser() )[ 0 ];
6445 species6.setRooted( true );
6446 gene6.setRooted( true );
6447 Phylogeny[] p6 = sdi_unrooted.infer( gene6, species6, false, true, true, true, 10 );
6448 if ( sdi_unrooted.getCount() != 1 ) {
6451 if ( !Test.isEqual( sdi_unrooted.getMinimalDiffInSubTreeHeights(), 0.0 ) ) {
6454 if ( !Test.isEqual( sdi_unrooted.getMinimalTreeHeight(), 0.375 ) ) {
6457 if ( sdi_unrooted.getMinimalDuplications() != 3 ) {
6460 if ( sdi_unrooted.getMinimalMappingCost() != Integer.MAX_VALUE ) {
6463 if ( !p6[ 0 ].getRoot().isDuplication() ) {
6466 if ( !p6[ 0 ].getNode( "4-5-6" ).isDuplication() ) {
6469 if ( !p6[ 0 ].getNode( "7-8-9" ).isDuplication() ) {
6472 if ( p6[ 0 ].getNode( "1-2" ).isDuplication() ) {
6475 if ( p6[ 0 ].getNode( "1-2-3" ).isDuplication() ) {
6478 if ( p6[ 0 ].getNode( "5-6" ).isDuplication() ) {
6481 if ( p6[ 0 ].getNode( "8-9" ).isDuplication() ) {
6484 if ( p6[ 0 ].getNode( "4-5-6-7-8-9" ).isDuplication() ) {
6488 final Phylogeny species7 = factory
6489 .create( "(((1:[&&NHX:S=1],5:[&&NHX:S=5])1-5,((4:[&&NHX:S=4],6:[&&NHX:S=6])4-6,2:[&&NHX:S=2])4-6-2)1-5-4-6-2,"
6490 + "((9:[&&NHX:S=9],3:[&&NHX:S=3])9-3,(8:[&&NHX:S=8],7:[&&NHX:S=7])8-7)9-3-8-7)",
6491 new NHXParser() )[ 0 ];
6492 final Phylogeny gene7 = factory
6493 .create( "((5:0.1[&&NHX:S=5],6:0.1[&&NHX:S=6])5-6:0.05[&&NHX:S=6],(4:0.1[&&NHX:S=4],"
6494 + "(((1:0.1[&&NHX:S=1],2:0.1[&&NHX:S=2])1-2:0.1[&&NHX:S=2],3:0.25[&&NHX:S=3])1-2-3:0.2[&&NHX:S=2],"
6495 + "(7:0.1[&&NHX:S=7],(8:0.1[&&NHX:S=8],"
6496 + "9:0.1[&&NHX:S=9])8-9:0.1[&&NHX:S=9])7-8-9:0.1[&&NHX:S=8])"
6497 + "4-5-6-7-8-9:0.1[&&NHX:S=5])4-5-6:0.05[&&NHX:S=5])",
6498 new NHXParser() )[ 0 ];
6499 species7.setRooted( true );
6500 gene7.setRooted( true );
6501 Phylogeny[] p7 = sdi_unrooted.infer( gene7, species7, true, true, true, true, 10 );
6502 if ( sdi_unrooted.getCount() != 1 ) {
6505 if ( !Test.isEqual( sdi_unrooted.getMinimalDiffInSubTreeHeights(), 0.0 ) ) {
6508 if ( !Test.isEqual( sdi_unrooted.getMinimalTreeHeight(), 0.375 ) ) {
6511 if ( sdi_unrooted.getMinimalDuplications() != 3 ) {
6514 if ( sdi_unrooted.getMinimalMappingCost() != 17 ) {
6517 if ( !p7[ 0 ].getRoot().isDuplication() ) {
6520 if ( !p7[ 0 ].getNode( "4-5-6" ).isDuplication() ) {
6523 if ( !p7[ 0 ].getNode( "7-8-9" ).isDuplication() ) {
6526 if ( p7[ 0 ].getNode( "1-2" ).isDuplication() ) {
6529 if ( p7[ 0 ].getNode( "1-2-3" ).isDuplication() ) {
6532 if ( p7[ 0 ].getNode( "5-6" ).isDuplication() ) {
6535 if ( p7[ 0 ].getNode( "8-9" ).isDuplication() ) {
6538 if ( p7[ 0 ].getNode( "4-5-6-7-8-9" ).isDuplication() ) {
6542 final Phylogeny species8 = factory
6543 .create( "(((1:[&&NHX:S=1],5:[&&NHX:S=5])1-5,((4:[&&NHX:S=4],6:[&&NHX:S=6])4-6,2:[&&NHX:S=2])4-6-2)1-5-4-6-2,"
6544 + "((9:[&&NHX:S=9],3:[&&NHX:S=3])9-3,(8:[&&NHX:S=8],7:[&&NHX:S=7])8-7)9-3-8-7)",
6545 new NHXParser() )[ 0 ];
6546 final Phylogeny gene8 = factory
6547 .create( "((5:0.1[&&NHX:S=5],6:0.1[&&NHX:S=6])5-6:0.05[&&NHX:S=6],(4:0.1[&&NHX:S=4],"
6548 + "(((1:0.1[&&NHX:S=1],2:0.1[&&NHX:S=2])1-2:0.1[&&NHX:S=2],3:0.25[&&NHX:S=3])1-2-3:0.2[&&NHX:S=2],"
6549 + "(7:0.1[&&NHX:S=7],(8:0.1[&&NHX:S=8],"
6550 + "9:0.1[&&NHX:S=9])8-9:0.1[&&NHX:S=9])7-8-9:0.1[&&NHX:S=8])"
6551 + "4-5-6-7-8-9:0.1[&&NHX:S=5])4-5-6:0.05[&&NHX:S=5])",
6552 new NHXParser() )[ 0 ];
6553 species8.setRooted( true );
6554 gene8.setRooted( true );
6555 Phylogeny[] p8 = sdi_unrooted.infer( gene8, species8, false, false, true, true, 10 );
6556 if ( sdi_unrooted.getCount() != 1 ) {
6559 if ( !Test.isEqual( sdi_unrooted.getMinimalDiffInSubTreeHeights(), 0.0 ) ) {
6562 if ( !Test.isEqual( sdi_unrooted.getMinimalTreeHeight(), 0.375 ) ) {
6565 if ( sdi_unrooted.getMinimalDuplications() != 3 ) {
6568 if ( sdi_unrooted.getMinimalMappingCost() != Integer.MAX_VALUE ) {
6571 if ( !p8[ 0 ].getRoot().isDuplication() ) {
6574 if ( !p8[ 0 ].getNode( "4-5-6" ).isDuplication() ) {
6577 if ( !p8[ 0 ].getNode( "7-8-9" ).isDuplication() ) {
6580 if ( p8[ 0 ].getNode( "1-2" ).isDuplication() ) {
6583 if ( p8[ 0 ].getNode( "1-2-3" ).isDuplication() ) {
6586 if ( p8[ 0 ].getNode( "5-6" ).isDuplication() ) {
6589 if ( p8[ 0 ].getNode( "8-9" ).isDuplication() ) {
6592 if ( p8[ 0 ].getNode( "4-5-6-7-8-9" ).isDuplication() ) {
6597 catch ( final Exception e ) {
6598 e.printStackTrace( System.out );
6604 private static boolean testSplit() {
6606 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
6607 final Phylogeny p0 = factory.create( "(((A,B,C),D),(E,(F,G)))R", new NHXParser() )[ 0 ];
6608 //Archaeopteryx.createApplication( p0 );
6609 final Set<PhylogenyNode> ex = new HashSet<PhylogenyNode>();
6610 ex.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6611 ex.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
6612 ex.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
6613 ex.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
6614 ex.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
6615 ex.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
6616 ex.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
6617 ex.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
6618 ex.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
6619 final TreeSplitMatrix s0 = new TreeSplitMatrix( p0, false, ex );
6620 // System.out.println( s0.toString() );
6622 Set<PhylogenyNode> query_nodes = new HashSet<PhylogenyNode>();
6623 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6624 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
6625 if ( s0.match( query_nodes ) ) {
6628 query_nodes = new HashSet<PhylogenyNode>();
6629 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6630 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
6631 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
6632 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
6633 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
6634 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
6635 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
6636 if ( !s0.match( query_nodes ) ) {
6640 query_nodes = new HashSet<PhylogenyNode>();
6641 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6642 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
6643 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
6644 if ( !s0.match( query_nodes ) ) {
6648 query_nodes = new HashSet<PhylogenyNode>();
6649 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
6650 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
6651 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
6652 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
6653 if ( !s0.match( query_nodes ) ) {
6657 query_nodes = new HashSet<PhylogenyNode>();
6658 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6659 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
6660 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
6661 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
6662 if ( !s0.match( query_nodes ) ) {
6666 query_nodes = new HashSet<PhylogenyNode>();
6667 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
6668 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
6669 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
6670 if ( !s0.match( query_nodes ) ) {
6674 query_nodes = new HashSet<PhylogenyNode>();
6675 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
6676 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
6677 if ( !s0.match( query_nodes ) ) {
6681 query_nodes = new HashSet<PhylogenyNode>();
6682 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
6683 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
6684 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
6685 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
6686 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6687 if ( !s0.match( query_nodes ) ) {
6691 query_nodes = new HashSet<PhylogenyNode>();
6692 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
6693 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
6694 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
6695 if ( !s0.match( query_nodes ) ) {
6699 query_nodes = new HashSet<PhylogenyNode>();
6700 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
6701 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
6702 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
6703 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
6704 if ( !s0.match( query_nodes ) ) {
6708 query_nodes = new HashSet<PhylogenyNode>();
6709 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
6710 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6711 if ( s0.match( query_nodes ) ) {
6715 query_nodes = new HashSet<PhylogenyNode>();
6716 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6717 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
6718 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
6719 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
6720 if ( s0.match( query_nodes ) ) {
6724 query_nodes = new HashSet<PhylogenyNode>();
6725 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
6726 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
6727 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
6728 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
6729 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
6730 if ( s0.match( query_nodes ) ) {
6734 query_nodes = new HashSet<PhylogenyNode>();
6735 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6736 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
6737 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
6738 if ( s0.match( query_nodes ) ) {
6742 query_nodes = new HashSet<PhylogenyNode>();
6743 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6744 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
6745 if ( s0.match( query_nodes ) ) {
6749 query_nodes = new HashSet<PhylogenyNode>();
6750 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6751 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
6752 if ( s0.match( query_nodes ) ) {
6756 query_nodes = new HashSet<PhylogenyNode>();
6757 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6758 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
6759 if ( s0.match( query_nodes ) ) {
6763 query_nodes = new HashSet<PhylogenyNode>();
6764 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6765 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
6766 if ( s0.match( query_nodes ) ) {
6770 query_nodes = new HashSet<PhylogenyNode>();
6771 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6772 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
6773 if ( s0.match( query_nodes ) ) {
6777 query_nodes = new HashSet<PhylogenyNode>();
6778 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6779 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
6780 if ( s0.match( query_nodes ) ) {
6784 query_nodes = new HashSet<PhylogenyNode>();
6785 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6786 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
6787 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
6788 if ( s0.match( query_nodes ) ) {
6792 query_nodes = new HashSet<PhylogenyNode>();
6793 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6794 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
6795 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
6796 if ( s0.match( query_nodes ) ) {
6800 query_nodes = new HashSet<PhylogenyNode>();
6801 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
6802 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
6803 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6804 if ( s0.match( query_nodes ) ) {
6808 query_nodes = new HashSet<PhylogenyNode>();
6809 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
6810 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
6811 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6812 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
6813 if ( s0.match( query_nodes ) ) {
6817 // query_nodes = new HashSet<PhylogenyNode>();
6818 // query_nodes.add( new PhylogenyNode( "X" ) );
6819 // query_nodes.add( new PhylogenyNode( "Y" ) );
6820 // query_nodes.add( new PhylogenyNode( "A" ) );
6821 // query_nodes.add( new PhylogenyNode( "B" ) );
6822 // query_nodes.add( new PhylogenyNode( "C" ) );
6823 // query_nodes.add( new PhylogenyNode( "D" ) );
6824 // query_nodes.add( new PhylogenyNode( "E" ) );
6825 // query_nodes.add( new PhylogenyNode( "F" ) );
6826 // query_nodes.add( new PhylogenyNode( "G" ) );
6827 // if ( !s0.match( query_nodes ) ) {
6830 // query_nodes = new HashSet<PhylogenyNode>();
6831 // query_nodes.add( new PhylogenyNode( "X" ) );
6832 // query_nodes.add( new PhylogenyNode( "Y" ) );
6833 // query_nodes.add( new PhylogenyNode( "A" ) );
6834 // query_nodes.add( new PhylogenyNode( "B" ) );
6835 // query_nodes.add( new PhylogenyNode( "C" ) );
6836 // if ( !s0.match( query_nodes ) ) {
6840 // query_nodes = new HashSet<PhylogenyNode>();
6841 // query_nodes.add( new PhylogenyNode( "X" ) );
6842 // query_nodes.add( new PhylogenyNode( "Y" ) );
6843 // query_nodes.add( new PhylogenyNode( "D" ) );
6844 // query_nodes.add( new PhylogenyNode( "E" ) );
6845 // query_nodes.add( new PhylogenyNode( "F" ) );
6846 // query_nodes.add( new PhylogenyNode( "G" ) );
6847 // if ( !s0.match( query_nodes ) ) {
6851 // query_nodes = new HashSet<PhylogenyNode>();
6852 // query_nodes.add( new PhylogenyNode( "X" ) );
6853 // query_nodes.add( new PhylogenyNode( "Y" ) );
6854 // query_nodes.add( new PhylogenyNode( "A" ) );
6855 // query_nodes.add( new PhylogenyNode( "B" ) );
6856 // query_nodes.add( new PhylogenyNode( "C" ) );
6857 // query_nodes.add( new PhylogenyNode( "D" ) );
6858 // if ( !s0.match( query_nodes ) ) {
6862 // query_nodes = new HashSet<PhylogenyNode>();
6863 // query_nodes.add( new PhylogenyNode( "X" ) );
6864 // query_nodes.add( new PhylogenyNode( "Y" ) );
6865 // query_nodes.add( new PhylogenyNode( "E" ) );
6866 // query_nodes.add( new PhylogenyNode( "F" ) );
6867 // query_nodes.add( new PhylogenyNode( "G" ) );
6868 // if ( !s0.match( query_nodes ) ) {
6872 // query_nodes = new HashSet<PhylogenyNode>();
6873 // query_nodes.add( new PhylogenyNode( "X" ) );
6874 // query_nodes.add( new PhylogenyNode( "Y" ) );
6875 // query_nodes.add( new PhylogenyNode( "F" ) );
6876 // query_nodes.add( new PhylogenyNode( "G" ) );
6877 // if ( !s0.match( query_nodes ) ) {
6881 query_nodes = new HashSet<PhylogenyNode>();
6882 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
6883 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
6884 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
6885 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
6886 if ( s0.match( query_nodes ) ) {
6890 query_nodes = new HashSet<PhylogenyNode>();
6891 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
6892 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
6893 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6894 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
6895 if ( s0.match( query_nodes ) ) {
6898 ///////////////////////////
6900 query_nodes = new HashSet<PhylogenyNode>();
6901 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
6902 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
6903 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6904 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
6905 if ( s0.match( query_nodes ) ) {
6909 query_nodes = new HashSet<PhylogenyNode>();
6910 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
6911 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
6912 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6913 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
6914 if ( s0.match( query_nodes ) ) {
6918 query_nodes = new HashSet<PhylogenyNode>();
6919 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
6920 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
6921 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6922 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
6923 if ( s0.match( query_nodes ) ) {
6927 query_nodes = new HashSet<PhylogenyNode>();
6928 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
6929 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
6930 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6931 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
6932 if ( s0.match( query_nodes ) ) {
6936 query_nodes = new HashSet<PhylogenyNode>();
6937 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
6938 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
6939 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6940 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
6941 if ( s0.match( query_nodes ) ) {
6945 query_nodes = new HashSet<PhylogenyNode>();
6946 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
6947 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6948 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
6949 if ( s0.match( query_nodes ) ) {
6953 query_nodes = new HashSet<PhylogenyNode>();
6954 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
6955 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
6956 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6957 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
6958 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
6959 if ( s0.match( query_nodes ) ) {
6963 query_nodes = new HashSet<PhylogenyNode>();
6964 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
6965 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
6966 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6967 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
6968 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
6969 if ( s0.match( query_nodes ) ) {
6973 query_nodes = new HashSet<PhylogenyNode>();
6974 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
6975 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
6976 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
6977 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
6978 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6979 if ( s0.match( query_nodes ) ) {
6983 query_nodes = new HashSet<PhylogenyNode>();
6984 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
6985 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
6986 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
6987 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
6988 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6989 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
6990 if ( s0.match( query_nodes ) ) {
6994 catch ( final Exception e ) {
6995 e.printStackTrace();
7001 private static boolean testSplitStrict() {
7003 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
7004 final Phylogeny p0 = factory.create( "(((A,B,C),D),(E,(F,G)))R", new NHXParser() )[ 0 ];
7005 final Set<PhylogenyNode> ex = new HashSet<PhylogenyNode>();
7006 ex.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7007 ex.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
7008 ex.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
7009 ex.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7010 ex.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7011 ex.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7012 ex.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7013 final TreeSplitMatrix s0 = new TreeSplitMatrix( p0, true, ex );
7014 Set<PhylogenyNode> query_nodes = new HashSet<PhylogenyNode>();
7015 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7016 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
7017 if ( s0.match( query_nodes ) ) {
7020 query_nodes = new HashSet<PhylogenyNode>();
7021 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7022 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
7023 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
7024 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7025 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7026 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7027 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7028 if ( !s0.match( query_nodes ) ) {
7032 query_nodes = new HashSet<PhylogenyNode>();
7033 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7034 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
7035 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
7036 if ( !s0.match( query_nodes ) ) {
7040 query_nodes = new HashSet<PhylogenyNode>();
7041 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7042 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7043 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7044 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7045 if ( !s0.match( query_nodes ) ) {
7049 query_nodes = new HashSet<PhylogenyNode>();
7050 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7051 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
7052 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
7053 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7054 if ( !s0.match( query_nodes ) ) {
7058 query_nodes = new HashSet<PhylogenyNode>();
7059 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7060 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7061 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7062 if ( !s0.match( query_nodes ) ) {
7066 query_nodes = new HashSet<PhylogenyNode>();
7067 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7068 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7069 if ( !s0.match( query_nodes ) ) {
7073 query_nodes = new HashSet<PhylogenyNode>();
7074 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7075 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7076 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
7077 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
7078 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7079 if ( !s0.match( query_nodes ) ) {
7083 query_nodes = new HashSet<PhylogenyNode>();
7084 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7085 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7086 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7087 if ( !s0.match( query_nodes ) ) {
7091 query_nodes = new HashSet<PhylogenyNode>();
7092 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7093 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7094 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7095 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7096 if ( !s0.match( query_nodes ) ) {
7100 query_nodes = new HashSet<PhylogenyNode>();
7101 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7102 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7103 if ( s0.match( query_nodes ) ) {
7107 query_nodes = new HashSet<PhylogenyNode>();
7108 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7109 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7110 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
7111 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
7112 if ( s0.match( query_nodes ) ) {
7116 query_nodes = new HashSet<PhylogenyNode>();
7117 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7118 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7119 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7120 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7121 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
7122 if ( s0.match( query_nodes ) ) {
7126 query_nodes = new HashSet<PhylogenyNode>();
7127 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7128 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
7129 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7130 if ( s0.match( query_nodes ) ) {
7134 query_nodes = new HashSet<PhylogenyNode>();
7135 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7136 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7137 if ( s0.match( query_nodes ) ) {
7141 query_nodes = new HashSet<PhylogenyNode>();
7142 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7143 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
7144 if ( s0.match( query_nodes ) ) {
7148 query_nodes = new HashSet<PhylogenyNode>();
7149 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7150 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
7151 if ( s0.match( query_nodes ) ) {
7155 query_nodes = new HashSet<PhylogenyNode>();
7156 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7157 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7158 if ( s0.match( query_nodes ) ) {
7162 query_nodes = new HashSet<PhylogenyNode>();
7163 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7164 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7165 if ( s0.match( query_nodes ) ) {
7169 query_nodes = new HashSet<PhylogenyNode>();
7170 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7171 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7172 if ( s0.match( query_nodes ) ) {
7176 query_nodes = new HashSet<PhylogenyNode>();
7177 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7178 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7179 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7180 if ( s0.match( query_nodes ) ) {
7184 query_nodes = new HashSet<PhylogenyNode>();
7185 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7186 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
7187 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7188 if ( s0.match( query_nodes ) ) {
7192 query_nodes = new HashSet<PhylogenyNode>();
7193 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7194 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7195 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7196 if ( s0.match( query_nodes ) ) {
7200 query_nodes = new HashSet<PhylogenyNode>();
7201 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7202 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7203 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7204 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7205 if ( s0.match( query_nodes ) ) {
7209 catch ( final Exception e ) {
7210 e.printStackTrace();
7216 private static boolean testSubtreeDeletion() {
7218 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
7219 final Phylogeny t1 = factory.create( "((A,B,C)abc,(D,E,F)def)r", new NHXParser() )[ 0 ];
7220 t1.deleteSubtree( t1.getNode( "A" ), false );
7221 if ( t1.getNumberOfExternalNodes() != 5 ) {
7224 t1.toNewHampshireX();
7225 t1.deleteSubtree( t1.getNode( "E" ), false );
7226 if ( t1.getNumberOfExternalNodes() != 4 ) {
7229 t1.toNewHampshireX();
7230 t1.deleteSubtree( t1.getNode( "F" ), false );
7231 if ( t1.getNumberOfExternalNodes() != 3 ) {
7234 t1.toNewHampshireX();
7235 t1.deleteSubtree( t1.getNode( "D" ), false );
7236 t1.toNewHampshireX();
7237 if ( t1.getNumberOfExternalNodes() != 3 ) {
7240 t1.deleteSubtree( t1.getNode( "def" ), false );
7241 t1.toNewHampshireX();
7242 if ( t1.getNumberOfExternalNodes() != 2 ) {
7245 t1.deleteSubtree( t1.getNode( "B" ), false );
7246 t1.toNewHampshireX();
7247 if ( t1.getNumberOfExternalNodes() != 1 ) {
7250 t1.deleteSubtree( t1.getNode( "C" ), false );
7251 t1.toNewHampshireX();
7252 if ( t1.getNumberOfExternalNodes() != 1 ) {
7255 t1.deleteSubtree( t1.getNode( "abc" ), false );
7256 t1.toNewHampshireX();
7257 if ( t1.getNumberOfExternalNodes() != 1 ) {
7260 t1.deleteSubtree( t1.getNode( "r" ), false );
7261 if ( t1.getNumberOfExternalNodes() != 0 ) {
7264 if ( !t1.isEmpty() ) {
7267 final Phylogeny t2 = factory.create( "(((1,2,3)A,B,C)abc,(D,E,F)def)r", new NHXParser() )[ 0 ];
7268 t2.deleteSubtree( t2.getNode( "A" ), false );
7269 t2.toNewHampshireX();
7270 if ( t2.getNumberOfExternalNodes() != 5 ) {
7273 t2.deleteSubtree( t2.getNode( "abc" ), false );
7274 t2.toNewHampshireX();
7275 if ( t2.getNumberOfExternalNodes() != 3 ) {
7278 t2.deleteSubtree( t2.getNode( "def" ), false );
7279 t2.toNewHampshireX();
7280 if ( t2.getNumberOfExternalNodes() != 1 ) {
7284 catch ( final Exception e ) {
7285 e.printStackTrace( System.out );
7291 private static boolean testSupportCount() {
7293 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
7294 final Phylogeny t0_1 = factory.create( "(((A,B),C),(D,E))", new NHXParser() )[ 0 ];
7295 final Phylogeny[] phylogenies_1 = factory.create( "(((A,B),C),(D,E)) " + "(((C,B),A),(D,E))"
7296 + "(((A,B),C),(D,E)) " + "(((A,B),C),(D,E))"
7297 + "(((A,B),C),(D,E))" + "(((C,B),A),(D,E))"
7298 + "(((E,B),D),(C,A))" + "(((C,B),A),(D,E))"
7299 + "(((A,B),C),(D,E))" + "(((A,B),C),(D,E))",
7301 SupportCount.count( t0_1, phylogenies_1, true, false );
7302 final Phylogeny t0_2 = factory.create( "(((((A,B),C),D),E),(F,G))", new NHXParser() )[ 0 ];
7303 final Phylogeny[] phylogenies_2 = factory.create( "(((((A,B),C),D),E),(F,G))"
7304 + "(((((A,B),C),D),E),((F,G),X))"
7305 + "(((((A,Y),B),C),D),((F,G),E))"
7306 + "(((((A,B),C),D),E),(F,G))"
7307 + "(((((A,B),C),D),E),(F,G))"
7308 + "(((((A,B),C),D),E),(F,G))"
7309 + "(((((A,B),C),D),E),(F,G),Z)"
7310 + "(((((A,B),C),D),E),(F,G))"
7311 + "((((((A,B),C),D),E),F),G)"
7312 + "(((((X,Y),F,G),E),((A,B),C)),D)",
7314 SupportCount.count( t0_2, phylogenies_2, true, false );
7315 final PhylogenyNodeIterator it = t0_2.iteratorPostorder();
7316 while ( it.hasNext() ) {
7317 final PhylogenyNode n = it.next();
7318 if ( !n.isExternal() && ( PhylogenyMethods.getConfidenceValue( n ) != 10 ) ) {
7322 final Phylogeny t0_3 = factory.create( "(((A,B)ab,C)abc,((D,E)de,F)def)", new NHXParser() )[ 0 ];
7323 final Phylogeny[] phylogenies_3 = factory.create( "(((A,B),C),((D,E),F))" + "(((A,C),B),((D,F),E))"
7324 + "(((C,A),B),((F,D),E))" + "(((A,B),F),((D,E),C))" + "(((((A,B),C),D),E),F)", new NHXParser() );
7325 SupportCount.count( t0_3, phylogenies_3, true, false );
7326 t0_3.reRoot( t0_3.getNode( "def" ).getId() );
7327 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "ab" ) ) != 3 ) {
7330 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "abc" ) ) != 4 ) {
7333 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "def" ) ) != 4 ) {
7336 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "de" ) ) != 2 ) {
7339 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "A" ) ) != 5 ) {
7342 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "B" ) ) != 5 ) {
7345 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "C" ) ) != 5 ) {
7348 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "D" ) ) != 5 ) {
7351 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "E" ) ) != 5 ) {
7354 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "F" ) ) != 5 ) {
7357 final Phylogeny t0_4 = factory.create( "(((((A,B)1,C)2,D)3,E)4,F)", new NHXParser() )[ 0 ];
7358 final Phylogeny[] phylogenies_4 = factory.create( "((((((A,X),C),B),D),E),F) "
7359 + "(((A,B,Z),C,Q),(((D,Y),E),F))", new NHXParser() );
7360 SupportCount.count( t0_4, phylogenies_4, true, false );
7361 t0_4.reRoot( t0_4.getNode( "F" ).getId() );
7362 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "1" ) ) != 1 ) {
7365 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "2" ) ) != 2 ) {
7368 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "3" ) ) != 1 ) {
7371 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "4" ) ) != 2 ) {
7374 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "A" ) ) != 2 ) {
7377 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "B" ) ) != 2 ) {
7380 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "C" ) ) != 2 ) {
7383 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "D" ) ) != 2 ) {
7386 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "E" ) ) != 2 ) {
7389 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "F" ) ) != 2 ) {
7392 Phylogeny a = factory.create( "(((((A,B)1,C)2,D)3,E)4,F)", new NHXParser() )[ 0 ];
7393 final Phylogeny b1 = factory.create( "(((((B,A)1,C)2,D)3,E)4,F)", new NHXParser() )[ 0 ];
7394 double d = SupportCount.compare( b1, a, true, true, true );
7395 if ( !Test.isEqual( d, 5.0 / 5.0 ) ) {
7398 a = factory.create( "(((((A,B)1,C)2,D)3,E)4,F)", new NHXParser() )[ 0 ];
7399 final Phylogeny b2 = factory.create( "(((((C,B)1,A)2,D)3,E)4,F)", new NHXParser() )[ 0 ];
7400 d = SupportCount.compare( b2, a, true, true, true );
7401 if ( !Test.isEqual( d, 4.0 / 5.0 ) ) {
7404 a = factory.create( "(((((A,B)1,C)2,D)3,E)4,F)", new NHXParser() )[ 0 ];
7405 final Phylogeny b3 = factory.create( "(((((F,C)1,A)2,B)3,D)4,E)", new NHXParser() )[ 0 ];
7406 d = SupportCount.compare( b3, a, true, true, true );
7407 if ( !Test.isEqual( d, 2.0 / 5.0 ) ) {
7410 a = factory.create( "(((((A,B)1,C)2,D)3,E)4,F)r", new NHXParser() )[ 0 ];
7411 final Phylogeny b4 = factory.create( "(((((F,C)1,A)2,B)3,D)4,E)r", new NHXParser() )[ 0 ];
7412 d = SupportCount.compare( b4, a, true, true, false );
7413 if ( !Test.isEqual( d, 1.0 / 5.0 ) ) {
7417 catch ( final Exception e ) {
7418 e.printStackTrace( System.out );
7424 private static boolean testSupportTransfer() {
7426 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
7427 final Phylogeny p1 = factory.create( "(((A,B)ab:97,C)abc:57,((D,E)de:10,(F,G)fg:50,(H,I)hi:64)defghi)",
7428 new NHXParser() )[ 0 ];
7429 final Phylogeny p2 = factory
7430 .create( "(((A:0.1,B:0.3)ab:0.4,C)abc:0.5,((D,E)de,(F,G)fg,(H,I)hi:0.59)defghi)", new NHXParser() )[ 0 ];
7431 if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "ab" ) ) >= 0.0 ) {
7434 if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "abc" ) ) >= 0.0 ) {
7437 support_transfer.moveBranchLengthsToBootstrap( p1 );
7438 support_transfer.transferSupportValues( p1, p2 );
7439 if ( p2.getNode( "ab" ).getDistanceToParent() != 0.4 ) {
7442 if ( p2.getNode( "abc" ).getDistanceToParent() != 0.5 ) {
7445 if ( p2.getNode( "hi" ).getDistanceToParent() != 0.59 ) {
7448 if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "ab" ) ) != 97 ) {
7451 if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "abc" ) ) != 57 ) {
7454 if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "de" ) ) != 10 ) {
7457 if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "fg" ) ) != 50 ) {
7460 if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "hi" ) ) != 64 ) {
7464 catch ( final Exception e ) {
7465 e.printStackTrace( System.out );
7471 private static boolean testTaxonomyAssigner() {
7473 String s0_str = "(((([&&NHX:S=A],[&&NHX:S=B])[&&NHX:S=AB],[&&NHX:S=C])[&&NHX:S=ABC],[&&NHX:S=D])[&&NHX:S=ABCD],[&&NHX:S=E])[&&NHX:S=ABCDE]";
7474 String g0_str = "((([&&NHX:S=A],[&&NHX:S=A],[&&NHX:S=A])a,[&&NHX:S=B])b,[&&NHX:S=C])c";
7475 Phylogeny s0 = ParserBasedPhylogenyFactory.getInstance().create( s0_str, new NHXParser() )[ 0 ];
7476 Phylogeny g0 = ParserBasedPhylogenyFactory.getInstance().create( g0_str, new NHXParser() )[ 0 ];
7477 s0.setRooted( true );
7478 g0.setRooted( true );
7479 TaxonomyAssigner.execute( g0, s0 );
7480 if ( !g0.getNode( "a" ).getNodeData().getTaxonomy().getScientificName().equals( "A" ) ) {
7483 if ( !g0.getNode( "b" ).getNodeData().getTaxonomy().getScientificName().equals( "AB" ) ) {
7486 if ( !g0.getNode( "c" ).getNodeData().getTaxonomy().getScientificName().equals( "ABC" ) ) {
7489 g0_str = "((([&&NHX:S=A],[&&NHX:S=A],[&&NHX:S=A])a,[&&NHX:S=A])b,[&&NHX:S=A])c";
7490 g0 = ParserBasedPhylogenyFactory.getInstance().create( g0_str, new NHXParser() )[ 0 ];
7491 g0.setRooted( true );
7492 TaxonomyAssigner.execute( g0, s0 );
7493 if ( !g0.getNode( "a" ).getNodeData().getTaxonomy().getScientificName().equals( "A" ) ) {
7496 if ( !g0.getNode( "b" ).getNodeData().getTaxonomy().getScientificName().equals( "A" ) ) {
7499 if ( !g0.getNode( "c" ).getNodeData().getTaxonomy().getScientificName().equals( "A" ) ) {
7502 g0_str = "((([&&NHX:S=A],[&&NHX:S=A],[&&NHX:S=B])a,[&&NHX:S=A])b,[&&NHX:S=A])c";
7503 g0 = ParserBasedPhylogenyFactory.getInstance().create( g0_str, new NHXParser() )[ 0 ];
7504 g0.setRooted( true );
7505 TaxonomyAssigner.execute( g0, s0 );
7506 if ( !g0.getNode( "a" ).getNodeData().getTaxonomy().getScientificName().equals( "AB" ) ) {
7509 if ( !g0.getNode( "b" ).getNodeData().getTaxonomy().getScientificName().equals( "AB" ) ) {
7512 if ( !g0.getNode( "c" ).getNodeData().getTaxonomy().getScientificName().equals( "AB" ) ) {
7515 g0_str = "((([&&NHX:S=A],[&&NHX:S=A],[&&NHX:S=B])a,[&&NHX:S=C])b,[&&NHX:S=A])c";
7516 g0 = ParserBasedPhylogenyFactory.getInstance().create( g0_str, new NHXParser() )[ 0 ];
7517 g0.setRooted( true );
7518 TaxonomyAssigner.execute( g0, s0 );
7519 if ( !g0.getNode( "a" ).getNodeData().getTaxonomy().getScientificName().equals( "AB" ) ) {
7522 if ( !g0.getNode( "b" ).getNodeData().getTaxonomy().getScientificName().equals( "ABC" ) ) {
7525 if ( !g0.getNode( "c" ).getNodeData().getTaxonomy().getScientificName().equals( "ABC" ) ) {
7528 g0_str = "((([&&NHX:S=A],[&&NHX:S=A],[&&NHX:S=B])a,[&&NHX:S=C])b,[&&NHX:S=D])c";
7529 g0 = ParserBasedPhylogenyFactory.getInstance().create( g0_str, new NHXParser() )[ 0 ];
7530 g0.setRooted( true );
7531 TaxonomyAssigner.execute( g0, s0 );
7532 if ( !g0.getNode( "a" ).getNodeData().getTaxonomy().getScientificName().equals( "AB" ) ) {
7535 if ( !g0.getNode( "b" ).getNodeData().getTaxonomy().getScientificName().equals( "ABC" ) ) {
7538 if ( !g0.getNode( "c" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCD" ) ) {
7541 g0_str = "((([&&NHX:S=A],[&&NHX:S=A],[&&NHX:S=E])a,[&&NHX:S=C])b,[&&NHX:S=D])c";
7542 g0 = ParserBasedPhylogenyFactory.getInstance().create( g0_str, new NHXParser() )[ 0 ];
7543 g0.setRooted( true );
7544 TaxonomyAssigner.execute( g0, s0 );
7545 if ( !g0.getNode( "a" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCDE" ) ) {
7548 if ( !g0.getNode( "b" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCDE" ) ) {
7551 if ( !g0.getNode( "c" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCDE" ) ) {
7554 g0_str = "((([&&NHX:S=A],[&&NHX:S=A],[&&NHX:S=E])a,[&&NHX:S=A])b,[&&NHX:S=A])c";
7555 g0 = ParserBasedPhylogenyFactory.getInstance().create( g0_str, new NHXParser() )[ 0 ];
7556 g0.setRooted( true );
7557 TaxonomyAssigner.execute( g0, s0 );
7558 if ( !g0.getNode( "a" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCDE" ) ) {
7561 if ( !g0.getNode( "b" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCDE" ) ) {
7564 if ( !g0.getNode( "c" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCDE" ) ) {
7567 s0_str = "(([&&NHX:S=A],[&&NHX:S=B],[&&NHX:S=C],[&&NHX:S=D])[&&NHX:S=ABCD],"
7568 + "([&&NHX:S=E],[&&NHX:S=F],[&&NHX:S=G],[&&NHX:S=H])[&&NHX:S=EFGH],"
7569 + "([&&NHX:S=I],[&&NHX:S=J],[&&NHX:S=K],[&&NHX:S=L])[&&NHX:S=IJKL], "
7570 + "([&&NHX:S=M],[&&NHX:S=N],[&&NHX:S=O],[&&NHX:S=P])[&&NHX:S=MNOP])[&&NHX:S=ROOT]";
7571 s0 = ParserBasedPhylogenyFactory.getInstance().create( s0_str, new NHXParser() )[ 0 ];
7572 s0.setRooted( true );
7573 g0_str = "(([&&NHX:S=A],[&&NHX:S=B],[&&NHX:S=C],[&&NHX:S=D])a,"
7574 + "([&&NHX:S=E],[&&NHX:S=F],[&&NHX:S=G],[&&NHX:S=H])b,"
7575 + "([&&NHX:S=I],[&&NHX:S=J],[&&NHX:S=K],[&&NHX:S=L])c, "
7576 + "([&&NHX:S=M],[&&NHX:S=N],[&&NHX:S=O],[&&NHX:S=P])d)r";
7577 g0 = ParserBasedPhylogenyFactory.getInstance().create( g0_str, new NHXParser() )[ 0 ];
7578 g0.setRooted( true );
7579 TaxonomyAssigner.execute( g0, s0 );
7580 if ( !g0.getNode( "a" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCD" ) ) {
7583 if ( !g0.getNode( "b" ).getNodeData().getTaxonomy().getScientificName().equals( "EFGH" ) ) {
7586 if ( !g0.getNode( "c" ).getNodeData().getTaxonomy().getScientificName().equals( "IJKL" ) ) {
7589 if ( !g0.getNode( "d" ).getNodeData().getTaxonomy().getScientificName().equals( "MNOP" ) ) {
7592 if ( !g0.getNode( "r" ).getNodeData().getTaxonomy().getScientificName().equals( "ROOT" ) ) {
7595 g0_str = "(([&&NHX:S=A],[&&NHX:S=B],[&&NHX:S=A],[&&NHX:S=B])a,"
7596 + "([&&NHX:S=E],[&&NHX:S=F],[&&NHX:S=F],[&&NHX:S=F])b,"
7597 + "([&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=I])c, "
7598 + "([&&NHX:S=M],[&&NHX:S=N],[&&NHX:S=O],[&&NHX:S=O])d)r";
7599 g0 = ParserBasedPhylogenyFactory.getInstance().create( g0_str, new NHXParser() )[ 0 ];
7600 g0.setRooted( true );
7601 TaxonomyAssigner.execute( g0, s0 );
7602 if ( !g0.getNode( "a" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCD" ) ) {
7605 if ( !g0.getNode( "b" ).getNodeData().getTaxonomy().getScientificName().equals( "EFGH" ) ) {
7608 if ( !g0.getNode( "c" ).getNodeData().getTaxonomy().getScientificName().equals( "IJKL" ) ) {
7611 if ( !g0.getNode( "d" ).getNodeData().getTaxonomy().getScientificName().equals( "MNOP" ) ) {
7614 if ( !g0.getNode( "r" ).getNodeData().getTaxonomy().getScientificName().equals( "ROOT" ) ) {
7617 g0_str = "(([&&NHX:S=A],[&&NHX:S=B],[&&NHX:S=A],[&&NHX:S=B])a,"
7618 + "([&&NHX:S=E],[&&NHX:S=F],[&&NHX:S=F],[&&NHX:S=F])b,"
7619 + "([&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L])c, "
7620 + "([&&NHX:S=M],[&&NHX:S=N],[&&NHX:S=A],[&&NHX:S=O])d)r";
7621 g0 = ParserBasedPhylogenyFactory.getInstance().create( g0_str, new NHXParser() )[ 0 ];
7622 g0.setRooted( true );
7623 TaxonomyAssigner.execute( g0, s0 );
7624 if ( !g0.getNode( "a" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCD" ) ) {
7627 if ( !g0.getNode( "b" ).getNodeData().getTaxonomy().getScientificName().equals( "EFGH" ) ) {
7630 if ( !g0.getNode( "c" ).getNodeData().getTaxonomy().getScientificName().equals( "L" ) ) {
7633 if ( !g0.getNode( "d" ).getNodeData().getTaxonomy().getScientificName().equals( "ROOT" ) ) {
7636 if ( !g0.getNode( "r" ).getNodeData().getTaxonomy().getScientificName().equals( "ROOT" ) ) {
7639 g0_str = "(([&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L])a,"
7640 + "([&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L])b,"
7641 + "([&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L])c, "
7642 + "([&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L])d)r";
7643 g0 = ParserBasedPhylogenyFactory.getInstance().create( g0_str, new NHXParser() )[ 0 ];
7644 g0.setRooted( true );
7645 TaxonomyAssigner.execute( g0, s0 );
7646 if ( !g0.getNode( "a" ).getNodeData().getTaxonomy().getScientificName().equals( "L" ) ) {
7649 if ( !g0.getNode( "b" ).getNodeData().getTaxonomy().getScientificName().equals( "L" ) ) {
7652 if ( !g0.getNode( "c" ).getNodeData().getTaxonomy().getScientificName().equals( "L" ) ) {
7655 if ( !g0.getNode( "d" ).getNodeData().getTaxonomy().getScientificName().equals( "L" ) ) {
7658 if ( !g0.getNode( "r" ).getNodeData().getTaxonomy().getScientificName().equals( "L" ) ) {
7661 g0_str = "((([&&NHX:S=A],[&&NHX:S=A],[&&NHX:S=A])a,[&&NHX:S=A])b,[&&NHX:S=A])c";
7662 g0 = ParserBasedPhylogenyFactory.getInstance().create( g0_str, new NHXParser() )[ 0 ];
7663 g0.setRooted( true );
7664 TaxonomyAssigner.execute( g0, s0 );
7665 if ( !g0.getNode( "a" ).getNodeData().getTaxonomy().getScientificName().equals( "A" ) ) {
7668 if ( !g0.getNode( "b" ).getNodeData().getTaxonomy().getScientificName().equals( "A" ) ) {
7671 if ( !g0.getNode( "c" ).getNodeData().getTaxonomy().getScientificName().equals( "A" ) ) {
7674 g0_str = "((([&&NHX:S=A],[&&NHX:S=A],[&&NHX:S=B])a,[&&NHX:S=I])b,[&&NHX:S=J])c";
7675 g0 = ParserBasedPhylogenyFactory.getInstance().create( g0_str, new NHXParser() )[ 0 ];
7676 g0.setRooted( true );
7677 TaxonomyAssigner.execute( g0, s0 );
7678 if ( !g0.getNode( "a" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCD" ) ) {
7681 if ( !g0.getNode( "b" ).getNodeData().getTaxonomy().getScientificName().equals( "ROOT" ) ) {
7684 if ( !g0.getNode( "c" ).getNodeData().getTaxonomy().getScientificName().equals( "ROOT" ) ) {
7687 g0_str = "(((([&&NHX:S=A],[&&NHX:S=B],[&&NHX:S=C],[&&NHX:S=D])a,"
7688 + "([&&NHX:S=D],[&&NHX:S=C],[&&NHX:S=B],[&&NHX:S=A])b)ab,"
7689 + "([&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L])c)abc, "
7690 + "([&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L])d)r";
7691 g0 = ParserBasedPhylogenyFactory.getInstance().create( g0_str, new NHXParser() )[ 0 ];
7692 g0.setRooted( true );
7693 TaxonomyAssigner.execute( g0, s0 );
7694 if ( !g0.getNode( "a" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCD" ) ) {
7697 if ( !g0.getNode( "b" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCD" ) ) {
7700 if ( !g0.getNode( "ab" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCD" ) ) {
7703 if ( !g0.getNode( "c" ).getNodeData().getTaxonomy().getScientificName().equals( "L" ) ) {
7706 if ( !g0.getNode( "abc" ).getNodeData().getTaxonomy().getScientificName().equals( "ROOT" ) ) {
7709 if ( !g0.getNode( "d" ).getNodeData().getTaxonomy().getScientificName().equals( "L" ) ) {
7712 if ( !g0.getNode( "r" ).getNodeData().getTaxonomy().getScientificName().equals( "ROOT" ) ) {
7715 g0_str = "(((([&&NHX:S=A],[&&NHX:S=A],[&&NHX:S=C],[&&NHX:S=D])a,"
7716 + "([&&NHX:S=D],[&&NHX:S=D],[&&NHX:S=B],[&&NHX:S=A])b)ab,"
7717 + "([&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L])c)abc, "
7718 + "([&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L])d)r";
7719 g0 = ParserBasedPhylogenyFactory.getInstance().create( g0_str, new NHXParser() )[ 0 ];
7720 g0.setRooted( true );
7721 TaxonomyAssigner.execute( g0, s0 );
7722 if ( !g0.getNode( "a" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCD" ) ) {
7725 if ( !g0.getNode( "b" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCD" ) ) {
7728 if ( !g0.getNode( "ab" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCD" ) ) {
7731 if ( !g0.getNode( "c" ).getNodeData().getTaxonomy().getScientificName().equals( "L" ) ) {
7734 if ( !g0.getNode( "abc" ).getNodeData().getTaxonomy().getScientificName().equals( "ROOT" ) ) {
7737 if ( !g0.getNode( "d" ).getNodeData().getTaxonomy().getScientificName().equals( "L" ) ) {
7740 if ( !g0.getNode( "r" ).getNodeData().getTaxonomy().getScientificName().equals( "ROOT" ) ) {
7743 g0_str = "(((([&&NHX:S=A],[&&NHX:S=A],[&&NHX:S=C],[&&NHX:S=D])a,"
7744 + "([&&NHX:S=D],[&&NHX:S=D],[&&NHX:S=B],[&&NHX:S=A])b)ab,"
7745 + "([&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L])c)abc, "
7746 + "([&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=A])d)r";
7747 g0 = ParserBasedPhylogenyFactory.getInstance().create( g0_str, new NHXParser() )[ 0 ];
7748 g0.setRooted( true );
7749 TaxonomyAssigner.execute( g0, s0 );
7750 if ( !g0.getNode( "a" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCD" ) ) {
7753 if ( !g0.getNode( "b" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCD" ) ) {
7756 if ( !g0.getNode( "ab" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCD" ) ) {
7759 if ( !g0.getNode( "c" ).getNodeData().getTaxonomy().getScientificName().equals( "L" ) ) {
7762 if ( !g0.getNode( "abc" ).getNodeData().getTaxonomy().getScientificName().equals( "ROOT" ) ) {
7765 if ( !g0.getNode( "d" ).getNodeData().getTaxonomy().getScientificName().equals( "ROOT" ) ) {
7768 if ( !g0.getNode( "r" ).getNodeData().getTaxonomy().getScientificName().equals( "ROOT" ) ) {
7771 g0_str = "(((([&&NHX:S=A],[&&NHX:S=A],[&&NHX:S=C],[&&NHX:S=D])a,"
7772 + "([&&NHX:S=D],[&&NHX:S=D],[&&NHX:S=B],[&&NHX:S=A])b)ab,"
7773 + "([&&NHX:S=A],[&&NHX:S=A],[&&NHX:S=A],[&&NHX:S=A])c)abc, "
7774 + "([&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=A])d)r";
7775 g0 = ParserBasedPhylogenyFactory.getInstance().create( g0_str, new NHXParser() )[ 0 ];
7776 g0.setRooted( true );
7777 TaxonomyAssigner.execute( g0, s0 );
7778 if ( !g0.getNode( "a" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCD" ) ) {
7781 if ( !g0.getNode( "b" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCD" ) ) {
7784 if ( !g0.getNode( "ab" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCD" ) ) {
7787 if ( !g0.getNode( "c" ).getNodeData().getTaxonomy().getScientificName().equals( "A" ) ) {
7790 if ( !g0.getNode( "abc" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCD" ) ) {
7793 if ( !g0.getNode( "d" ).getNodeData().getTaxonomy().getScientificName().equals( "ROOT" ) ) {
7796 if ( !g0.getNode( "r" ).getNodeData().getTaxonomy().getScientificName().equals( "ROOT" ) ) {
7799 s0_str = "(([&&NHX:S=A],[&&NHX:S=B],[&&NHX:S=C],[&&NHX:S=D]),"
7800 + "([&&NHX:S=E],[&&NHX:S=F],[&&NHX:S=G],[&&NHX:S=H]),"
7801 + "([&&NHX:S=I],[&&NHX:S=J],[&&NHX:S=K],[&&NHX:S=L]), "
7802 + "([&&NHX:S=M],[&&NHX:S=N],[&&NHX:S=O],[&&NHX:S=P]))";
7803 s0 = ParserBasedPhylogenyFactory.getInstance().create( s0_str, new NHXParser() )[ 0 ];
7804 s0.setRooted( true );
7805 g0_str = "(((([&&NHX:S=A],[&&NHX:S=A],[&&NHX:S=C],[&&NHX:S=D])a,"
7806 + "([&&NHX:S=D],[&&NHX:S=D],[&&NHX:S=B],[&&NHX:S=A])b)ab,"
7807 + "([&&NHX:S=A],[&&NHX:S=A],[&&NHX:S=A],[&&NHX:S=A])c)abc, "
7808 + "([&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=A])d)r";
7809 g0 = ParserBasedPhylogenyFactory.getInstance().create( g0_str, new NHXParser() )[ 0 ];
7810 g0.setRooted( true );
7811 TaxonomyAssigner.execute( g0, s0 );
7812 if ( g0.getNode( "a" ).getNodeData().isHasTaxonomy() ) {
7815 if ( !g0.getNode( "c" ).getNodeData().getTaxonomy().getScientificName().equals( "A" ) ) {
7819 catch ( final Exception e ) {
7820 e.printStackTrace( System.out );
7826 private static boolean testUniprotTaxonomySearch() {
7828 List<UniProtTaxonomy> results = UniProtWsTools
7829 .getTaxonomiesFromCommonNameStrict( "starlet sea anemone", 10 );
7830 if ( results.size() != 1 ) {
7833 if ( !results.get( 0 ).getCode().equals( "NEMVE" ) ) {
7836 if ( !results.get( 0 ).getCommonName().equalsIgnoreCase( "starlet sea anemone" ) ) {
7839 if ( !results.get( 0 ).getId().equalsIgnoreCase( "45351" ) ) {
7842 if ( !results.get( 0 ).getRank().equalsIgnoreCase( "species" ) ) {
7845 if ( !results.get( 0 ).getScientificName().equals( "Nematostella vectensis" ) ) {
7849 results = UniProtWsTools.getTaxonomiesFromScientificNameStrict( "Nematostella vectensis", 10 );
7850 if ( results.size() != 1 ) {
7853 if ( !results.get( 0 ).getCode().equals( "NEMVE" ) ) {
7856 if ( !results.get( 0 ).getCommonName().equalsIgnoreCase( "starlet sea anemone" ) ) {
7859 if ( !results.get( 0 ).getId().equalsIgnoreCase( "45351" ) ) {
7862 if ( !results.get( 0 ).getRank().equalsIgnoreCase( "species" ) ) {
7865 if ( !results.get( 0 ).getScientificName().equals( "Nematostella vectensis" ) ) {
7869 results = UniProtWsTools.getTaxonomiesFromId( "45351", 10 );
7870 if ( results.size() != 1 ) {
7873 if ( !results.get( 0 ).getCode().equals( "NEMVE" ) ) {
7876 if ( !results.get( 0 ).getCommonName().equalsIgnoreCase( "starlet sea anemone" ) ) {
7879 if ( !results.get( 0 ).getId().equalsIgnoreCase( "45351" ) ) {
7882 if ( !results.get( 0 ).getRank().equalsIgnoreCase( "species" ) ) {
7885 if ( !results.get( 0 ).getScientificName().equals( "Nematostella vectensis" ) ) {
7889 results = UniProtWsTools.getTaxonomiesFromTaxonomyCode( "NEMVE", 10 );
7890 if ( results.size() != 1 ) {
7893 if ( !results.get( 0 ).getCode().equals( "NEMVE" ) ) {
7896 if ( !results.get( 0 ).getCommonName().equalsIgnoreCase( "starlet sea anemone" ) ) {
7899 if ( !results.get( 0 ).getId().equalsIgnoreCase( "45351" ) ) {
7902 if ( !results.get( 0 ).getRank().equalsIgnoreCase( "species" ) ) {
7905 if ( !results.get( 0 ).getScientificName().equals( "Nematostella vectensis" ) ) {
7908 if ( !results.get( 0 ).getLineage().get( 1 ).equals( "Eukaryota" ) ) {
7911 if ( !results.get( 0 ).getLineage().get( 2 ).equals( "Metazoa" ) ) {
7914 if ( !results.get( 0 ).getLineage().get( results.get( 0 ).getLineage().size() - 1 )
7915 .equals( "Nematostella vectensis" ) ) {
7916 System.out.println( results.get( 0 ).getLineage() );
7920 catch ( final IOException e ) {
7921 System.out.println();
7922 System.out.println( "the following might be due to absence internet connection:" );
7923 e.printStackTrace( System.out );
7926 catch ( final Exception e ) {
7932 private static boolean testEmblEntryRetrieval() {
7933 //The format for GenBank Accession numbers are:
7934 //Nucleotide: 1 letter + 5 numerals OR 2 letters + 6 numerals
7935 //Protein: 3 letters + 5 numerals
7936 //http://www.ncbi.nlm.nih.gov/Sequin/acc.html
7937 if ( !DatabaseTools.parseGenbankAccessor( "AY423861" ).equals( "AY423861" ) ) {
7940 if ( !DatabaseTools.parseGenbankAccessor( ".AY423861." ).equals( "AY423861" ) ) {
7943 if ( DatabaseTools.parseGenbankAccessor( "AAY423861" ) != null ) {
7946 if ( DatabaseTools.parseGenbankAccessor( "AY4238612" ) != null ) {
7949 if ( DatabaseTools.parseGenbankAccessor( "AAY4238612" ) != null ) {
7952 if ( DatabaseTools.parseGenbankAccessor( "Y423861" ) != null ) {
7955 if ( !DatabaseTools.parseGenbankAccessor( "S12345" ).equals( "S12345" ) ) {
7958 if ( !DatabaseTools.parseGenbankAccessor( "|S12345|" ).equals( "S12345" ) ) {
7961 if ( DatabaseTools.parseGenbankAccessor( "|S123456" ) != null ) {
7964 if ( DatabaseTools.parseGenbankAccessor( "ABC123456" ) != null ) {
7967 if ( !DatabaseTools.parseGenbankAccessor( "ABC12345" ).equals( "ABC12345" ) ) {
7970 if ( !DatabaseTools.parseGenbankAccessor( "&ABC12345&" ).equals( "ABC12345" ) ) {
7973 if ( DatabaseTools.parseGenbankAccessor( "ABCD12345" ) != null ) {
7979 private static boolean testUniprotEntryRetrieval() {
7980 if ( !UniProtWsTools.parseUniProtAccessor( "P12345" ).equals( "P12345" ) ) {
7983 if ( UniProtWsTools.parseUniProtAccessor( "EP12345" ) != null ) {
7986 if ( UniProtWsTools.parseUniProtAccessor( "3 4P12345" ) != null ) {
7989 if ( UniProtWsTools.parseUniProtAccessor( "P12345E" ) != null ) {
7992 if ( UniProtWsTools.parseUniProtAccessor( "P123455" ) != null ) {
7995 if ( UniProtWsTools.parseUniProtAccessor( "EP12345E" ) != null ) {
7998 if ( UniProtWsTools.parseUniProtAccessor( "AY423861" ) != null ) {
8001 if ( !UniProtWsTools.parseUniProtAccessor( "P1DDD5" ).equals( "P1DDD5" ) ) {
8004 if ( UniProtWsTools.parseUniProtAccessor( "P1DDDD" ) != null ) {
8007 if ( !UniProtWsTools.parseUniProtAccessor( "P1234X/P12345/12-42" ).equals( "P12345" ) ) {
8010 if ( !UniProtWsTools.parseUniProtAccessor( "P1234X P12345 12-42" ).equals( "P12345" ) ) {
8013 if ( !UniProtWsTools.parseUniProtAccessor( "P12345/12-42" ).equals( "P12345" ) ) {
8016 if ( !UniProtWsTools.parseUniProtAccessor( "P1234X/P12345" ).equals( "P12345" ) ) {
8020 final SequenceDatabaseEntry entry = UniProtWsTools.obtainUniProtEntry( "P12345", 200 );
8021 if ( !entry.getAccession().equals( "P12345" ) ) {
8024 if ( !entry.getTaxonomyScientificName().equals( "Oryctolagus cuniculus" ) ) {
8027 if ( !entry.getSequenceName().equals( "Aspartate aminotransferase, mitochondrial" ) ) {
8030 if ( !entry.getSequenceSymbol().equals( "GOT2" ) ) {
8033 if ( !entry.getTaxonomyIdentifier().equals( "9986" ) ) {
8037 catch ( final IOException e ) {
8038 System.out.println();
8039 System.out.println( "the following might be due to absence internet connection:" );
8040 e.printStackTrace( System.out );
8043 catch ( final Exception e ) {
8049 private static boolean testWabiTxSearch() {
8052 result = TxSearch.searchSimple( "nematostella" );
8053 result = TxSearch.getTxId( "nematostella" );
8054 if ( !result.equals( "45350" ) ) {
8057 result = TxSearch.getTxName( "45350" );
8058 if ( !result.equals( "Nematostella" ) ) {
8061 result = TxSearch.getTxId( "nematostella vectensis" );
8062 if ( !result.equals( "45351" ) ) {
8065 result = TxSearch.getTxName( "45351" );
8066 if ( !result.equals( "Nematostella vectensis" ) ) {
8069 result = TxSearch.getTxId( "Bacillus subtilis subsp. subtilis str. N170" );
8070 if ( !result.equals( "536089" ) ) {
8073 result = TxSearch.getTxName( "536089" );
8074 if ( !result.equals( "Bacillus subtilis subsp. subtilis str. N170" ) ) {
8077 final List<String> queries = new ArrayList<String>();
8078 queries.add( "Campylobacter coli" );
8079 queries.add( "Escherichia coli" );
8080 queries.add( "Arabidopsis" );
8081 queries.add( "Trichoplax" );
8082 queries.add( "Samanea saman" );
8083 queries.add( "Kluyveromyces marxianus" );
8084 queries.add( "Bacillus subtilis subsp. subtilis str. N170" );
8085 queries.add( "Bornavirus parrot/PDD/2008" );
8086 final List<RANKS> ranks = new ArrayList<RANKS>();
8087 ranks.add( RANKS.SUPERKINGDOM );
8088 ranks.add( RANKS.KINGDOM );
8089 ranks.add( RANKS.FAMILY );
8090 ranks.add( RANKS.GENUS );
8091 ranks.add( RANKS.TRIBE );
8092 result = TxSearch.searchLineage( queries, ranks );
8093 result = TxSearch.searchParam( "Homo sapiens", TAX_NAME_CLASS.ALL, TAX_RANK.SPECIES, 10, true );
8094 result = TxSearch.searchParam( "Samanea saman", TAX_NAME_CLASS.SCIENTIFIC_NAME, TAX_RANK.ALL, 10, true );
8096 catch ( final Exception e ) {
8097 System.out.println();
8098 System.out.println( "the following might be due to absence internet connection:" );
8099 e.printStackTrace( System.out );
8105 private static boolean testAminoAcidSequence() {
8107 final Sequence aa1 = BasicSequence.createAaSequence( "aa1", "aAklm-?xX*z$#" );
8108 if ( aa1.getLength() != 13 ) {
8111 if ( aa1.getResidueAt( 0 ) != 'A' ) {
8114 if ( aa1.getResidueAt( 2 ) != 'K' ) {
8117 if ( !new String( aa1.getMolecularSequence() ).equals( "AAKLM-XXX*ZXX" ) ) {
8120 final Sequence aa2 = BasicSequence.createAaSequence( "aa3", "ARNDCQEGHILKMFPSTWYVX*-BZOJU" );
8121 if ( !new String( aa2.getMolecularSequence() ).equals( "ARNDCQEGHILKMFPSTWYVX*-BZXXU" ) ) {
8124 final Sequence dna1 = BasicSequence.createDnaSequence( "dna1", "ACGTUX*-?RYMKWSN" );
8125 if ( !new String( dna1.getMolecularSequence() ).equals( "ACGTNN*-NRYMKWSN" ) ) {
8128 final Sequence rna1 = BasicSequence.createRnaSequence( "rna1", "..ACGUTX*-?RYMKWSN" );
8129 if ( !new String( rna1.getMolecularSequence() ).equals( "--ACGUNN*-NRYMKWSN" ) ) {
8133 catch ( final Exception e ) {
8134 e.printStackTrace();
8140 private static boolean testCreateBalancedPhylogeny() {
8142 final Phylogeny p0 = DevelopmentTools.createBalancedPhylogeny( 6, 5 );
8143 if ( p0.getRoot().getNumberOfDescendants() != 5 ) {
8146 if ( p0.getNumberOfExternalNodes() != 15625 ) {
8149 final Phylogeny p1 = DevelopmentTools.createBalancedPhylogeny( 2, 10 );
8150 if ( p1.getRoot().getNumberOfDescendants() != 10 ) {
8153 if ( p1.getNumberOfExternalNodes() != 100 ) {
8157 catch ( final Exception e ) {
8158 e.printStackTrace();
8164 private static boolean testFastaParser() {
8166 if ( !FastaParser.isLikelyFasta( new FileInputStream( PATH_TO_TEST_DATA + "fasta_0.fasta" ) ) ) {
8169 if ( FastaParser.isLikelyFasta( new FileInputStream( PATH_TO_TEST_DATA + "msa_3.txt" ) ) ) {
8172 final Msa msa_0 = FastaParser.parseMsa( new FileInputStream( PATH_TO_TEST_DATA + "fasta_0.fasta" ) );
8173 if ( !msa_0.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "ACGTGKXFMFDMXEXXXSFMFMF" ) ) {
8176 if ( !msa_0.getIdentifier( 0 ).equals( "one dumb" ) ) {
8179 if ( !msa_0.getSequenceAsString( 1 ).toString().equalsIgnoreCase( "DKXASDFXSFXFKFKSXDFKSLX" ) ) {
8182 if ( !msa_0.getSequenceAsString( 2 ).toString().equalsIgnoreCase( "SXDFKSXLFSFPWEXPRXWXERR" ) ) {
8185 if ( !msa_0.getSequenceAsString( 3 ).toString().equalsIgnoreCase( "AAAAAAAAAAAAAAAAAAAAAAA" ) ) {
8188 if ( !msa_0.getSequenceAsString( 4 ).toString().equalsIgnoreCase( "DDDDDDDDDDDDDDDDDDDDAXF" ) ) {
8192 catch ( final Exception e ) {
8193 e.printStackTrace();
8199 private static boolean testGeneralMsaParser() {
8201 final String msa_str_0 = "seq1 abcd\n\nseq2 efgh\n";
8202 final Msa msa_0 = GeneralMsaParser.parse( new ByteArrayInputStream( msa_str_0.getBytes() ) );
8203 final String msa_str_1 = "seq_1 abc\nseq2 ghi\nseq_1 def\nseq2 jkm\n";
8204 final Msa msa_1 = GeneralMsaParser.parse( new ByteArrayInputStream( msa_str_1.getBytes() ) );
8205 final String msa_str_2 = "seq1 abc\nseq2 ghi\n\ndef\njkm\n";
8206 final Msa msa_2 = GeneralMsaParser.parse( new ByteArrayInputStream( msa_str_2.getBytes() ) );
8207 final String msa_str_3 = "seq1 abc\n def\nseq2 ghi\n jkm\n";
8208 final Msa msa_3 = GeneralMsaParser.parse( new ByteArrayInputStream( msa_str_3.getBytes() ) );
8209 final Msa msa_4 = GeneralMsaParser.parse( new FileInputStream( PATH_TO_TEST_DATA + "msa_1.txt" ) );
8210 if ( !msa_4.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "abcdefeeeeeeeexx" ) ) {
8213 if ( !msa_4.getSequenceAsString( 1 ).toString().equalsIgnoreCase( "efghixffffffffyy" ) ) {
8216 if ( !msa_4.getSequenceAsString( 2 ).toString().equalsIgnoreCase( "klmnxphhhhhhhhzz" ) ) {
8219 final Msa msa_5 = GeneralMsaParser.parse( new FileInputStream( PATH_TO_TEST_DATA + "msa_2.txt" ) );
8220 if ( !msa_5.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "abcdefxx" ) ) {
8223 if ( !msa_5.getSequenceAsString( 1 ).toString().equalsIgnoreCase( "efghixyy" ) ) {
8226 if ( !msa_5.getSequenceAsString( 2 ).toString().equalsIgnoreCase( "klmnxpzz" ) ) {
8229 final Msa msa_6 = GeneralMsaParser.parse( new FileInputStream( PATH_TO_TEST_DATA + "msa_3.txt" ) );
8230 if ( !msa_6.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "abcdefeeeeeeeexx" ) ) {
8233 if ( !msa_6.getSequenceAsString( 1 ).toString().equalsIgnoreCase( "efghixffffffffyy" ) ) {
8236 if ( !msa_6.getSequenceAsString( 2 ).toString().equalsIgnoreCase( "klmnxphhhhhhhhzz" ) ) {
8240 catch ( final Exception e ) {
8241 e.printStackTrace();
8247 private static boolean testMafft() {
8249 final List<String> opts = new ArrayList<String>();
8250 opts.add( "--maxiterate" );
8252 opts.add( "--localpair" );
8253 opts.add( "--quiet" );
8255 final MsaInferrer mafft = Mafft.createInstance();
8256 msa = mafft.infer( new File( PATH_TO_TEST_DATA + "ncbi_sn.fasta" ), opts );
8257 if ( ( msa == null ) || ( msa.getLength() < 10 ) || ( msa.getNumberOfSequences() != 19 ) ) {
8261 catch ( final Exception e ) {
8262 e.printStackTrace( System.out );
8268 private static boolean testNextNodeWithCollapsing() {
8270 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
8272 List<PhylogenyNode> ext = new ArrayList<PhylogenyNode>();
8273 final StringBuffer sb0 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h))fgh)cdefgh)abcdefgh" );
8274 final Phylogeny t0 = factory.create( sb0, new NHXParser() )[ 0 ];
8275 t0.getNode( "cd" ).setCollapse( true );
8276 t0.getNode( "cde" ).setCollapse( true );
8277 n = t0.getFirstExternalNode();
8278 while ( n != null ) {
8280 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8282 if ( !ext.get( 0 ).getName().equals( "a" ) ) {
8285 if ( !ext.get( 1 ).getName().equals( "b" ) ) {
8288 if ( !ext.get( 2 ).getName().equals( "cde" ) ) {
8291 if ( !ext.get( 3 ).getName().equals( "f" ) ) {
8294 if ( !ext.get( 4 ).getName().equals( "g" ) ) {
8297 if ( !ext.get( 5 ).getName().equals( "h" ) ) {
8301 final StringBuffer sb1 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h))fgh)cdefgh)abcdefgh" );
8302 final Phylogeny t1 = factory.create( sb1, new NHXParser() )[ 0 ];
8303 t1.getNode( "ab" ).setCollapse( true );
8304 t1.getNode( "cd" ).setCollapse( true );
8305 t1.getNode( "cde" ).setCollapse( true );
8306 n = t1.getNode( "ab" );
8307 ext = new ArrayList<PhylogenyNode>();
8308 while ( n != null ) {
8310 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8312 if ( !ext.get( 0 ).getName().equals( "ab" ) ) {
8315 if ( !ext.get( 1 ).getName().equals( "cde" ) ) {
8318 if ( !ext.get( 2 ).getName().equals( "f" ) ) {
8321 if ( !ext.get( 3 ).getName().equals( "g" ) ) {
8324 if ( !ext.get( 4 ).getName().equals( "h" ) ) {
8330 final StringBuffer sb2 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
8331 final Phylogeny t2 = factory.create( sb2, new NHXParser() )[ 0 ];
8332 t2.getNode( "ab" ).setCollapse( true );
8333 t2.getNode( "cd" ).setCollapse( true );
8334 t2.getNode( "cde" ).setCollapse( true );
8335 t2.getNode( "c" ).setCollapse( true );
8336 t2.getNode( "d" ).setCollapse( true );
8337 t2.getNode( "e" ).setCollapse( true );
8338 t2.getNode( "gh" ).setCollapse( true );
8339 n = t2.getNode( "ab" );
8340 ext = new ArrayList<PhylogenyNode>();
8341 while ( n != null ) {
8343 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8345 if ( !ext.get( 0 ).getName().equals( "ab" ) ) {
8348 if ( !ext.get( 1 ).getName().equals( "cde" ) ) {
8351 if ( !ext.get( 2 ).getName().equals( "f" ) ) {
8354 if ( !ext.get( 3 ).getName().equals( "gh" ) ) {
8360 final StringBuffer sb3 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
8361 final Phylogeny t3 = factory.create( sb3, new NHXParser() )[ 0 ];
8362 t3.getNode( "ab" ).setCollapse( true );
8363 t3.getNode( "cd" ).setCollapse( true );
8364 t3.getNode( "cde" ).setCollapse( true );
8365 t3.getNode( "c" ).setCollapse( true );
8366 t3.getNode( "d" ).setCollapse( true );
8367 t3.getNode( "e" ).setCollapse( true );
8368 t3.getNode( "gh" ).setCollapse( true );
8369 t3.getNode( "fgh" ).setCollapse( true );
8370 n = t3.getNode( "ab" );
8371 ext = new ArrayList<PhylogenyNode>();
8372 while ( n != null ) {
8374 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8376 if ( !ext.get( 0 ).getName().equals( "ab" ) ) {
8379 if ( !ext.get( 1 ).getName().equals( "cde" ) ) {
8382 if ( !ext.get( 2 ).getName().equals( "fgh" ) ) {
8388 final StringBuffer sb4 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
8389 final Phylogeny t4 = factory.create( sb4, new NHXParser() )[ 0 ];
8390 t4.getNode( "ab" ).setCollapse( true );
8391 t4.getNode( "cd" ).setCollapse( true );
8392 t4.getNode( "cde" ).setCollapse( true );
8393 t4.getNode( "c" ).setCollapse( true );
8394 t4.getNode( "d" ).setCollapse( true );
8395 t4.getNode( "e" ).setCollapse( true );
8396 t4.getNode( "gh" ).setCollapse( true );
8397 t4.getNode( "fgh" ).setCollapse( true );
8398 t4.getNode( "abcdefgh" ).setCollapse( true );
8399 n = t4.getNode( "abcdefgh" );
8400 if ( n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes() != null ) {
8405 final StringBuffer sb5 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h))fgh)cdefgh)abcdefgh" );
8406 final Phylogeny t5 = factory.create( sb5, new NHXParser() )[ 0 ];
8408 n = t5.getFirstExternalNode();
8409 while ( n != null ) {
8411 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8413 if ( ext.size() != 8 ) {
8416 if ( !ext.get( 0 ).getName().equals( "a" ) ) {
8419 if ( !ext.get( 1 ).getName().equals( "b" ) ) {
8422 if ( !ext.get( 2 ).getName().equals( "c" ) ) {
8425 if ( !ext.get( 3 ).getName().equals( "d" ) ) {
8428 if ( !ext.get( 4 ).getName().equals( "e" ) ) {
8431 if ( !ext.get( 5 ).getName().equals( "f" ) ) {
8434 if ( !ext.get( 6 ).getName().equals( "g" ) ) {
8437 if ( !ext.get( 7 ).getName().equals( "h" ) ) {
8442 final StringBuffer sb6 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h))fgh)cdefgh)abcdefgh" );
8443 final Phylogeny t6 = factory.create( sb6, new NHXParser() )[ 0 ];
8445 t6.getNode( "ab" ).setCollapse( true );
8446 n = t6.getNode( "ab" );
8447 while ( n != null ) {
8449 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8451 if ( ext.size() != 7 ) {
8454 if ( !ext.get( 0 ).getName().equals( "ab" ) ) {
8457 if ( !ext.get( 1 ).getName().equals( "c" ) ) {
8460 if ( !ext.get( 2 ).getName().equals( "d" ) ) {
8463 if ( !ext.get( 3 ).getName().equals( "e" ) ) {
8466 if ( !ext.get( 4 ).getName().equals( "f" ) ) {
8469 if ( !ext.get( 5 ).getName().equals( "g" ) ) {
8472 if ( !ext.get( 6 ).getName().equals( "h" ) ) {
8477 final StringBuffer sb7 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h))fgh)cdefgh)abcdefgh" );
8478 final Phylogeny t7 = factory.create( sb7, new NHXParser() )[ 0 ];
8480 t7.getNode( "cd" ).setCollapse( true );
8481 n = t7.getNode( "a" );
8482 while ( n != null ) {
8484 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8486 if ( ext.size() != 7 ) {
8489 if ( !ext.get( 0 ).getName().equals( "a" ) ) {
8492 if ( !ext.get( 1 ).getName().equals( "b" ) ) {
8495 if ( !ext.get( 2 ).getName().equals( "cd" ) ) {
8498 if ( !ext.get( 3 ).getName().equals( "e" ) ) {
8501 if ( !ext.get( 4 ).getName().equals( "f" ) ) {
8504 if ( !ext.get( 5 ).getName().equals( "g" ) ) {
8507 if ( !ext.get( 6 ).getName().equals( "h" ) ) {
8512 final StringBuffer sb8 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h))fgh)cdefgh)abcdefgh" );
8513 final Phylogeny t8 = factory.create( sb8, new NHXParser() )[ 0 ];
8515 t8.getNode( "cd" ).setCollapse( true );
8516 t8.getNode( "c" ).setCollapse( true );
8517 t8.getNode( "d" ).setCollapse( true );
8518 n = t8.getNode( "a" );
8519 while ( n != null ) {
8521 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8523 if ( ext.size() != 7 ) {
8526 if ( !ext.get( 0 ).getName().equals( "a" ) ) {
8529 if ( !ext.get( 1 ).getName().equals( "b" ) ) {
8532 if ( !ext.get( 2 ).getName().equals( "cd" ) ) {
8533 System.out.println( "2 fail" );
8536 if ( !ext.get( 3 ).getName().equals( "e" ) ) {
8539 if ( !ext.get( 4 ).getName().equals( "f" ) ) {
8542 if ( !ext.get( 5 ).getName().equals( "g" ) ) {
8545 if ( !ext.get( 6 ).getName().equals( "h" ) ) {
8550 final StringBuffer sb9 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
8551 final Phylogeny t9 = factory.create( sb9, new NHXParser() )[ 0 ];
8553 t9.getNode( "gh" ).setCollapse( true );
8554 n = t9.getNode( "a" );
8555 while ( n != null ) {
8557 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8559 if ( ext.size() != 7 ) {
8562 if ( !ext.get( 0 ).getName().equals( "a" ) ) {
8565 if ( !ext.get( 1 ).getName().equals( "b" ) ) {
8568 if ( !ext.get( 2 ).getName().equals( "c" ) ) {
8571 if ( !ext.get( 3 ).getName().equals( "d" ) ) {
8574 if ( !ext.get( 4 ).getName().equals( "e" ) ) {
8577 if ( !ext.get( 5 ).getName().equals( "f" ) ) {
8580 if ( !ext.get( 6 ).getName().equals( "gh" ) ) {
8585 final StringBuffer sb10 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
8586 final Phylogeny t10 = factory.create( sb10, new NHXParser() )[ 0 ];
8588 t10.getNode( "gh" ).setCollapse( true );
8589 t10.getNode( "g" ).setCollapse( true );
8590 t10.getNode( "h" ).setCollapse( true );
8591 n = t10.getNode( "a" );
8592 while ( n != null ) {
8594 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8596 if ( ext.size() != 7 ) {
8599 if ( !ext.get( 0 ).getName().equals( "a" ) ) {
8602 if ( !ext.get( 1 ).getName().equals( "b" ) ) {
8605 if ( !ext.get( 2 ).getName().equals( "c" ) ) {
8608 if ( !ext.get( 3 ).getName().equals( "d" ) ) {
8611 if ( !ext.get( 4 ).getName().equals( "e" ) ) {
8614 if ( !ext.get( 5 ).getName().equals( "f" ) ) {
8617 if ( !ext.get( 6 ).getName().equals( "gh" ) ) {
8622 final StringBuffer sb11 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
8623 final Phylogeny t11 = factory.create( sb11, new NHXParser() )[ 0 ];
8625 t11.getNode( "gh" ).setCollapse( true );
8626 t11.getNode( "fgh" ).setCollapse( true );
8627 n = t11.getNode( "a" );
8628 while ( n != null ) {
8630 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8632 if ( ext.size() != 6 ) {
8635 if ( !ext.get( 0 ).getName().equals( "a" ) ) {
8638 if ( !ext.get( 1 ).getName().equals( "b" ) ) {
8641 if ( !ext.get( 2 ).getName().equals( "c" ) ) {
8644 if ( !ext.get( 3 ).getName().equals( "d" ) ) {
8647 if ( !ext.get( 4 ).getName().equals( "e" ) ) {
8650 if ( !ext.get( 5 ).getName().equals( "fgh" ) ) {
8655 final StringBuffer sb12 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
8656 final Phylogeny t12 = factory.create( sb12, new NHXParser() )[ 0 ];
8658 t12.getNode( "gh" ).setCollapse( true );
8659 t12.getNode( "fgh" ).setCollapse( true );
8660 t12.getNode( "g" ).setCollapse( true );
8661 t12.getNode( "h" ).setCollapse( true );
8662 t12.getNode( "f" ).setCollapse( true );
8663 n = t12.getNode( "a" );
8664 while ( n != null ) {
8666 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8668 if ( ext.size() != 6 ) {
8671 if ( !ext.get( 0 ).getName().equals( "a" ) ) {
8674 if ( !ext.get( 1 ).getName().equals( "b" ) ) {
8677 if ( !ext.get( 2 ).getName().equals( "c" ) ) {
8680 if ( !ext.get( 3 ).getName().equals( "d" ) ) {
8683 if ( !ext.get( 4 ).getName().equals( "e" ) ) {
8686 if ( !ext.get( 5 ).getName().equals( "fgh" ) ) {
8691 final StringBuffer sb13 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
8692 final Phylogeny t13 = factory.create( sb13, new NHXParser() )[ 0 ];
8694 t13.getNode( "ab" ).setCollapse( true );
8695 t13.getNode( "b" ).setCollapse( true );
8696 t13.getNode( "fgh" ).setCollapse( true );
8697 t13.getNode( "gh" ).setCollapse( true );
8698 n = t13.getNode( "ab" );
8699 while ( n != null ) {
8701 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8703 if ( ext.size() != 5 ) {
8706 if ( !ext.get( 0 ).getName().equals( "ab" ) ) {
8709 if ( !ext.get( 1 ).getName().equals( "c" ) ) {
8712 if ( !ext.get( 2 ).getName().equals( "d" ) ) {
8715 if ( !ext.get( 3 ).getName().equals( "e" ) ) {
8718 if ( !ext.get( 4 ).getName().equals( "fgh" ) ) {
8723 final StringBuffer sb14 = new StringBuffer( "((a,b,0)ab,(((c,d)cd,e)cde,(f,(g,h,1,2)gh,0)fgh)cdefgh)abcdefgh" );
8724 final Phylogeny t14 = factory.create( sb14, new NHXParser() )[ 0 ];
8726 t14.getNode( "ab" ).setCollapse( true );
8727 t14.getNode( "a" ).setCollapse( true );
8728 t14.getNode( "fgh" ).setCollapse( true );
8729 t14.getNode( "gh" ).setCollapse( true );
8730 n = t14.getNode( "ab" );
8731 while ( n != null ) {
8733 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8735 if ( ext.size() != 5 ) {
8738 if ( !ext.get( 0 ).getName().equals( "ab" ) ) {
8741 if ( !ext.get( 1 ).getName().equals( "c" ) ) {
8744 if ( !ext.get( 2 ).getName().equals( "d" ) ) {
8747 if ( !ext.get( 3 ).getName().equals( "e" ) ) {
8750 if ( !ext.get( 4 ).getName().equals( "fgh" ) ) {
8755 final StringBuffer sb15 = new StringBuffer( "((a,b,0)ab,(((c,d)cd,e)cde,x,(f,(g,h,1,2)gh,0)fgh)cdefgh)abcdefgh" );
8756 final Phylogeny t15 = factory.create( sb15, new NHXParser() )[ 0 ];
8758 t15.getNode( "ab" ).setCollapse( true );
8759 t15.getNode( "a" ).setCollapse( true );
8760 t15.getNode( "fgh" ).setCollapse( true );
8761 t15.getNode( "gh" ).setCollapse( true );
8762 n = t15.getNode( "ab" );
8763 while ( n != null ) {
8765 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8767 if ( ext.size() != 6 ) {
8770 if ( !ext.get( 0 ).getName().equals( "ab" ) ) {
8773 if ( !ext.get( 1 ).getName().equals( "c" ) ) {
8776 if ( !ext.get( 2 ).getName().equals( "d" ) ) {
8779 if ( !ext.get( 3 ).getName().equals( "e" ) ) {
8782 if ( !ext.get( 4 ).getName().equals( "x" ) ) {
8785 if ( !ext.get( 5 ).getName().equals( "fgh" ) ) {
8790 final StringBuffer sb16 = new StringBuffer( "((a,b,0)ab,(((c,d)cd,e)cde,x,(f,(g,h,1,2)gh,0)fgh)cdefgh)abcdefgh" );
8791 final Phylogeny t16 = factory.create( sb16, new NHXParser() )[ 0 ];
8793 t16.getNode( "ab" ).setCollapse( true );
8794 t16.getNode( "a" ).setCollapse( true );
8795 t16.getNode( "fgh" ).setCollapse( true );
8796 t16.getNode( "gh" ).setCollapse( true );
8797 t16.getNode( "cd" ).setCollapse( true );
8798 t16.getNode( "cde" ).setCollapse( true );
8799 t16.getNode( "d" ).setCollapse( true );
8800 t16.getNode( "x" ).setCollapse( true );
8801 n = t16.getNode( "ab" );
8802 while ( n != null ) {
8804 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8806 if ( ext.size() != 4 ) {
8809 if ( !ext.get( 0 ).getName().equals( "ab" ) ) {
8812 if ( !ext.get( 1 ).getName().equals( "cde" ) ) {
8815 if ( !ext.get( 2 ).getName().equals( "x" ) ) {
8818 if ( !ext.get( 3 ).getName().equals( "fgh" ) ) {
8822 catch ( final Exception e ) {
8823 e.printStackTrace( System.out );